0s autopkgtest [08:20:54]: starting date and time: 2024-03-27 08:20:54+0000 0s autopkgtest [08:20:54]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [08:20:54]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s6hj3rkg/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed --apt-upgrade bowtie2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.12.2-0ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-10.secgroup --name adt-noble-ppc64el-bowtie2-20240327-082054-juju-7f2275-prod-proposed-migration-environment-3-fe0deefa-2ed6-48a8-b6d9-6791046a4d48 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 343s autopkgtest [08:26:37]: testbed dpkg architecture: ppc64el 343s autopkgtest [08:26:37]: testbed apt version: 2.7.12 343s autopkgtest [08:26:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 344s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 345s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3964 kB] 346s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 346s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B] 346s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [55.4 kB] 346s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [702 kB] 346s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 346s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 346s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 346s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4217 kB] 347s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 347s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [62.2 kB] 347s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 350s Fetched 9637 kB in 3s (2811 kB/s) 350s Reading package lists... 352s Reading package lists... 352s Building dependency tree... 352s Reading state information... 352s Calculating upgrade... 352s The following packages will be upgraded: 352s psmisc 352s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 352s Need to get 192 kB of archives. 352s After this operation, 28.7 kB disk space will be freed. 352s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el psmisc ppc64el 23.7-1 [192 kB] 353s Fetched 192 kB in 1s (333 kB/s) 353s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70156 files and directories currently installed.) 353s Preparing to unpack .../psmisc_23.7-1_ppc64el.deb ... 353s Unpacking psmisc (23.7-1) over (23.6-2) ... 353s Setting up psmisc (23.7-1) ... 353s Processing triggers for man-db (2.12.0-3) ... 354s Reading package lists... 354s Building dependency tree... 354s Reading state information... 354s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded. 355s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 355s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 355s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 355s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 356s Reading package lists... 356s Reading package lists... 356s Building dependency tree... 356s Reading state information... 357s Calculating upgrade... 357s The following packages were automatically installed and are no longer required: 357s libaio1 libnetplan0 python3-distutils python3-lib2to3 357s Use 'sudo apt autoremove' to remove them. 357s The following packages will be REMOVED: 357s libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1 357s libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11 357s libhogweed6 libmagic1 libnettle8 libnpth0 libnvme1 libparted2 libperl5.38 357s libpng16-16 libpsl5 libreadline8 libreiserfscore0 libssl3 libtirpc3 liburcu8 357s libuv1 357s The following NEW packages will be installed: 357s bpfcc-tools bpftrace fontconfig-config fonts-dejavu-core fonts-dejavu-mono 357s ieee-data libaio1t64 libapt-pkg6.0t64 libarchive13t64 libatm1t64 libbpfcc 357s libc-dev-bin libc-devtools libc6-dev libclang-cpp18 libclang1-18 357s libcrypt-dev libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libdeflate0 357s libdw1t64 libelf1t64 libext2fs2t64 libfontconfig1 libgd3 libgdbm-compat4t64 357s libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64 357s libjbig0 libjpeg-turbo8 libjpeg8 liblerc4 libllvm18 libmagic1t64 libnetplan1 357s libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64 libperl5.38t64 357s libpng16-16t64 libpsl5t64 libreadline8t64 libreiserfscore0t64 libsharpyuv0 357s libssl3t64 libtiff6 libtirpc3t64 libunwind8 liburcu8t64 libuv1t64 libwebp7 357s libxpm4 linux-headers-6.8.0-20 linux-headers-6.8.0-20-generic 357s linux-image-6.8.0-20-generic linux-libc-dev linux-modules-6.8.0-20-generic 357s linux-modules-extra-6.8.0-20-generic linux-tools-6.8.0-20 357s linux-tools-6.8.0-20-generic linux-tools-common manpages manpages-dev 357s python3-bpfcc python3-netaddr rpcsvc-proto ubuntu-kernel-accessories 357s xdg-user-dirs 357s The following packages will be upgraded: 357s apparmor apt apt-utils base-files bash bc bind9-dnsutils bind9-host 357s bind9-libs binutils binutils-common binutils-powerpc64le-linux-gnu bolt 357s bsdextrautils bsdutils btrfs-progs coreutils cryptsetup-bin curl dbus 357s dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common 357s dbus-user-session dhcpcd-base dirmngr dmsetup dpkg dpkg-dev e2fsprogs 357s e2fsprogs-l10n eject fdisk file ftp fwupd gawk gcc-13-base gcc-14-base 357s gir1.2-girepository-2.0 gir1.2-glib-2.0 gnupg gnupg-l10n gnupg-utils gpg 357s gpg-agent gpg-wks-client gpgconf gpgsm gpgv groff-base grub-common 357s grub-ieee1275 grub-ieee1275-bin grub2-common ibverbs-providers 357s inetutils-telnet info initramfs-tools initramfs-tools-bin 357s initramfs-tools-core install-info iproute2 jq keyboxd kmod kpartx 357s krb5-locales libapparmor1 libaudit-common libaudit1 libbinutils libblkid1 357s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 357s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 357s libblockdev3 libbpf1 libbrotli1 libcap-ng0 libcom-err2 libcryptsetup12 357s libctf-nobfd0 libctf0 libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 357s libdpkg-perl libevent-core-2.1-7 libexpat1 libfdisk1 libfido2-1 libfreetype6 357s libftdi1-2 libfwupd2 libgcc-s1 libgirepository-1.0-1 libglib2.0-data 357s libgssapi-krb5-2 libgudev-1.0-0 libgusb2 libibverbs1 libjcat1 libjq1 357s libjson-glib-1.0-0 libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3 357s libkrb5support0 libldap-common libldap2 liblocale-gettext-perl liblzma5 357s libmagic-mgc libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14 357s libnsl2 libnss-systemd libpam-modules libpam-modules-bin libpam-runtime 357s libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0 357s libpolkit-gobject-1-0 libproc2-0 libprotobuf-c1 libpython3-stdlib 357s libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal 357s libpython3.12-stdlib libqmi-glib5 libqmi-proxy libqrtr-glib0 librtmp1 357s libsasl2-2 libsasl2-modules libsasl2-modules-db libseccomp2 libselinux1 357s libsemanage-common libsemanage2 libsframe1 libslang2 libsmartcols1 357s libsqlite3-0 libss2 libssh-4 libstdc++6 libsystemd-shared libsystemd0 357s libtext-charwidth-perl libtext-iconv-perl libtirpc-common libudev1 357s libudisks2-0 libusb-1.0-0 libuuid1 libvolume-key1 libxml2 libxmlb2 libxmuu1 357s linux-generic linux-headers-generic linux-headers-virtual 357s linux-image-generic linux-image-virtual linux-virtual logsave lshw lsof 357s man-db motd-news-config mount mtr-tiny multipath-tools netplan-generator 357s netplan.io openssh-client openssh-server openssh-sftp-server openssl parted 357s perl perl-base perl-modules-5.38 pinentry-curses plymouth 357s plymouth-theme-ubuntu-text procps python-apt-common python3 python3-apt 357s python3-cryptography python3-dbus python3-distutils python3-gdbm python3-gi 357s python3-lib2to3 python3-minimal python3-netplan python3-pkg-resources 357s python3-pyrsistent python3-setuptools python3-typing-extensions python3-yaml 357s python3.11 python3.11-minimal python3.12 python3.12-minimal readline-common 357s rsync rsyslog shared-mime-info sudo systemd systemd-dev systemd-resolved 357s systemd-sysv systemd-timesyncd tcpdump telnet tnftp ubuntu-pro-client 357s ubuntu-pro-client-l10n udev udisks2 usb.ids util-linux uuid-runtime 357s vim-common vim-tiny wget xxd xz-utils zlib1g 357s 248 upgraded, 73 newly installed, 28 to remove and 0 not upgraded. 357s Need to get 390 MB of archives. 357s After this operation, 640 MB of additional disk space will be used. 357s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el motd-news-config all 13ubuntu8 [5098 B] 357s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el base-files ppc64el 13ubuntu8 [74.5 kB] 357s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bash ppc64el 5.2.21-2ubuntu3 [977 kB] 358s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdutils ppc64el 1:2.39.3-9ubuntu2 [98.3 kB] 358s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el coreutils ppc64el 9.4-3ubuntu3 [1523 kB] 358s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libudisks2-0 ppc64el 2.10.1-6 [182 kB] 358s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el udisks2 ppc64el 2.10.1-6 [344 kB] 358s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el shared-mime-info ppc64el 2.4-1build1 [481 kB] 358s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gir1.2-girepository-2.0 ppc64el 1.79.1-1ubuntu6 [24.8 kB] 358s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gir1.2-glib-2.0 ppc64el 2.79.3-3ubuntu5 [182 kB] 358s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgirepository-1.0-1 ppc64el 1.79.1-1ubuntu6 [93.8 kB] 358s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-gi ppc64el 3.47.0-3build1 [261 kB] 359s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-dbus ppc64el 1.3.2-5build2 [107 kB] 359s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnetplan1 ppc64el 1.0-1 [136 kB] 359s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-netplan ppc64el 1.0-1 [21.8 kB] 359s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el netplan-generator ppc64el 1.0-1 [59.2 kB] 359s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el initramfs-tools-bin ppc64el 0.142ubuntu23 [21.0 kB] 359s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el initramfs-tools-core all 0.142ubuntu23 [50.1 kB] 359s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el initramfs-tools all 0.142ubuntu23 [9058 B] 359s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el netplan.io ppc64el 1.0-1 [66.2 kB] 359s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxmlb2 ppc64el 0.3.15-1build1 [82.6 kB] 359s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgpgme11t64 ppc64el 1.18.0-4.1ubuntu3 [173 kB] 359s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libvolume-key1 ppc64el 0.3.12-7build1 [47.9 kB] 359s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libqrtr-glib0 ppc64el 1.2.2-1ubuntu3 [18.3 kB] 359s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libqmi-glib5 ppc64el 1.35.2-0ubuntu1 [966 kB] 359s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libqmi-proxy ppc64el 1.35.2-0ubuntu1 [6208 B] 359s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpolkit-agent-1-0 ppc64el 124-1ubuntu1 [18.8 kB] 359s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpolkit-gobject-1-0 ppc64el 124-1ubuntu1 [52.7 kB] 359s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmm-glib0 ppc64el 1.23.4-0ubuntu1 [282 kB] 359s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmbim-glib4 ppc64el 1.31.2-0ubuntu2 [253 kB] 359s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmbim-proxy ppc64el 1.31.2-0ubuntu2 [6274 B] 359s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjson-glib-1.0-common all 1.8.0-2build1 [4210 B] 359s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjson-glib-1.0-0 ppc64el 1.8.0-2build1 [73.6 kB] 359s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgusb2 ppc64el 0.4.8-1build1 [43.0 kB] 359s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgudev-1.0-0 ppc64el 1:238-3ubuntu2 [15.8 kB] 359s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el tnftp ppc64el 20230507-2build1 [116 kB] 359s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el tcpdump ppc64el 4.99.4-3ubuntu2 [543 kB] 359s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsystemd0 ppc64el 255.4-1ubuntu5 [526 kB] 359s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-dev all 255.4-1ubuntu5 [103 kB] 359s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnss-systemd ppc64el 255.4-1ubuntu5 [208 kB] 359s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libudev1 ppc64el 255.4-1ubuntu5 [200 kB] 359s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 360s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd ppc64el 255.4-1ubuntu5 [3771 kB] 360s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el udev ppc64el 255.4-1ubuntu5 [2038 kB] 360s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-sysv ppc64el 255.4-1ubuntu5 [11.9 kB] 360s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-systemd ppc64el 255.4-1ubuntu5 [304 kB] 360s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-timesyncd ppc64el 255.4-1ubuntu5 [37.9 kB] 360s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsystemd-shared ppc64el 255.4-1ubuntu5 [2351 kB] 360s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-resolved ppc64el 255.4-1ubuntu5 [346 kB] 360s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el sudo ppc64el 1.9.15p5-3ubuntu3 [1005 kB] 360s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el rsync ppc64el 3.2.7-1build1 [487 kB] 361s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-cryptography ppc64el 41.0.7-4build2 [860 kB] 361s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 361s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssh-sftp-server ppc64el 1:9.6p1-3ubuntu11 [43.7 kB] 361s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssh-client ppc64el 1:9.6p1-3ubuntu11 [1112 kB] 361s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssh-server ppc64el 1:9.6p1-3ubuntu11 [627 kB] 361s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssh-4 ppc64el 0.10.6-2build1 [234 kB] 361s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-modules ppc64el 2.1.28+dfsg1-5ubuntu1 [83.1 kB] 361s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.12 ppc64el 3.12.2-4build3 [645 kB] 361s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.12-minimal ppc64el 3.12.2-4build3 [2447 kB] 361s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.12-minimal ppc64el 3.12.2-4build3 [836 kB] 361s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el grub-ieee1275 ppc64el 2.12-1ubuntu5 [63.1 kB] 361s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el grub2-common ppc64el 2.12-1ubuntu5 [752 kB] 361s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el grub-common ppc64el 2.12-1ubuntu5 [2356 kB] 361s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el grub-ieee1275-bin ppc64el 2.12-1ubuntu5 [687 kB] 361s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libparted2t64 ppc64el 3.6-3.1build2 [184 kB] 361s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el parted ppc64el 3.6-3.1build2 [58.9 kB] 361s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.11 ppc64el 3.11.8-1build4 [589 kB] 361s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.11-minimal ppc64el 3.11.8-1build4 [2292 kB] 361s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.11-minimal ppc64el 3.11.8-1build4 [846 kB] 361s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.11-stdlib ppc64el 3.11.8-1build4 [1977 kB] 362s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gnupg-utils ppc64el 2.4.4-2ubuntu15 [123 kB] 362s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg-agent ppc64el 2.4.4-2ubuntu15 [275 kB] 362s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg-wks-client ppc64el 2.4.4-2ubuntu15 [85.0 kB] 362s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg ppc64el 2.4.4-2ubuntu15 [706 kB] 362s Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el libnpth0t64 ppc64el 1.6-3.1 [8864 B] 362s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgv ppc64el 2.4.4-2ubuntu15 [198 kB] 362s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dirmngr ppc64el 2.4.4-2ubuntu15 [391 kB] 362s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gnupg all 2.4.4-2ubuntu15 [359 kB] 362s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el keyboxd ppc64el 2.4.4-2ubuntu15 [94.3 kB] 362s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgconf ppc64el 2.4.4-2ubuntu15 [115 kB] 362s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgsm ppc64el 2.4.4-2ubuntu15 [292 kB] 362s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libreadline8t64 ppc64el 8.2-4 [182 kB] 362s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gawk ppc64el 1:5.2.1-2build2 [528 kB] 362s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el fdisk ppc64el 2.39.3-9ubuntu2 [132 kB] 362s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bc ppc64el 1.07.1-3ubuntu2 [93.2 kB] 362s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.12-stdlib ppc64el 3.12.2-4build3 [2082 kB] 362s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-base ppc64el 5.38.2-3.2 [1916 kB] 362s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 362s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-gdbm ppc64el 3.12.2-3ubuntu1.1 [19.8 kB] 362s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el man-db ppc64el 2.12.0-3build4 [1274 kB] 362s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm6t64 ppc64el 1.23-5.1 [41.9 kB] 362s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm-compat4t64 ppc64el 1.23-5.1 [6972 B] 362s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libperl5.38t64 ppc64el 5.38.2-3.2 [4957 kB] 362s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl ppc64el 5.38.2-3.2 [231 kB] 362s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdb5.3t64 ppc64el 5.3.28+dfsg2-6 [875 kB] 362s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-modules-db ppc64el 2.1.28+dfsg1-5ubuntu1 [23.4 kB] 362s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-2 ppc64el 2.1.28+dfsg1-5ubuntu1 [68.0 kB] 362s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnvme1t64 ppc64el 1.8-3 [98.2 kB] 362s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el wget ppc64el 1.21.4-1ubuntu2 [382 kB] 362s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl4t64 ppc64el 8.5.0-2ubuntu8 [428 kB] 362s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el curl ppc64el 8.5.0-2ubuntu8 [234 kB] 363s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpsl5t64 ppc64el 0.21.2-1.1 [59.0 kB] 363s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libarchive13t64 ppc64el 3.7.2-1.1ubuntu2 [518 kB] 363s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el fwupd ppc64el 1.9.15-2 [4634 kB] 363s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl3t64-gnutls ppc64el 8.5.0-2ubuntu8 [419 kB] 363s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfwupd2 ppc64el 1.9.15-2 [136 kB] 363s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev3 ppc64el 3.1.0-1build1 [55.2 kB] 363s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-utils3 ppc64el 3.1.0-1build1 [20.3 kB] 363s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-swap3 ppc64el 3.1.0-1build1 [8616 B] 363s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-part3 ppc64el 3.1.0-1build1 [17.5 kB] 363s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-nvme3 ppc64el 3.1.0-1build1 [20.1 kB] 363s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-mdraid3 ppc64el 3.1.0-1build1 [14.3 kB] 363s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-loop3 ppc64el 3.1.0-1build1 [7742 B] 363s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B] 363s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el logsave ppc64el 1.47.0-2.4~exp1ubuntu2 [22.9 kB] 363s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libext2fs2t64 ppc64el 1.47.0-2.4~exp1ubuntu2 [270 kB] 363s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el e2fsprogs ppc64el 1.47.0-2.4~exp1ubuntu2 [663 kB] 363s Get:119 http://ftpmaster.internal/ubuntu noble/main ppc64el libreiserfscore0t64 ppc64el 1:3.6.27-7.1 [92.7 kB] 363s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el btrfs-progs ppc64el 6.6.3-1.1build1 [1352 kB] 363s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-fs3 ppc64el 3.1.0-1build1 [41.2 kB] 363s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-crypto3 ppc64el 3.1.0-1build1 [22.5 kB] 363s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bolt ppc64el 0.9.6-2build1 [171 kB] 363s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-0t64 ppc64el 2.79.3-3ubuntu5 [1773 kB] 363s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjcat1 ppc64el 0.2.0-2build2 [40.0 kB] 363s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libldap2 ppc64el 2.6.7+dfsg-1~exp1ubuntu6 [233 kB] 363s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ubuntu-pro-client-l10n ppc64el 31.2.2 [19.4 kB] 363s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ubuntu-pro-client ppc64el 31.2.2 [215 kB] 363s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-apt ppc64el 2.7.7 [181 kB] 363s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el apt-utils ppc64el 2.7.14 [226 kB] 363s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapt-pkg6.0t64 ppc64el 2.7.14 [1063 kB] 363s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnettle8t64 ppc64el 3.9.1-2.2 [226 kB] 363s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libhogweed6t64 ppc64el 3.9.1-2.2 [208 kB] 363s Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgnutls30t64 ppc64el 3.8.3-1.1ubuntu2 [1154 kB] 363s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el apt ppc64el 2.7.14 [1401 kB] 363s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build6 [64.4 kB] 363s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblzma5 ppc64el 5.6.0-0.2 [156 kB] 363s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblkid1 ppc64el 2.39.3-9ubuntu2 [155 kB] 363s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el kmod ppc64el 31+20240202-2ubuntu4 [122 kB] 363s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkmod2 ppc64el 31+20240202-2ubuntu4 [64.4 kB] 363s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libselinux1 ppc64el 3.5-2ubuntu1 [101 kB] 363s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libaudit-common all 1:3.1.2-2.1 [5674 B] 363s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcap-ng0 ppc64el 0.8.4-2build1 [16.2 kB] 363s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libaudit1 ppc64el 1:3.1.2-2.1 [52.8 kB] 364s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam0g ppc64el 1.5.3-5ubuntu3 [75.7 kB] 364s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules-bin ppc64el 1.5.3-5ubuntu3 [57.9 kB] 364s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules ppc64el 1.5.3-5ubuntu3 [320 kB] 364s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] 364s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB] 364s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-user-session ppc64el 1.14.10-4ubuntu2 [9960 B] 364s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapparmor1 ppc64el 4.0.0-beta3-0ubuntu2 [55.0 kB] 364s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libexpat1 ppc64el 2.6.1-2 [101 kB] 364s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB] 364s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-bin ppc64el 1.14.10-4ubuntu2 [48.1 kB] 364s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus ppc64el 1.14.10-4ubuntu2 [26.9 kB] 364s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-daemon ppc64el 1.14.10-4ubuntu2 [136 kB] 364s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdbus-1-3 ppc64el 1.14.10-4ubuntu2 [244 kB] 364s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.185-3ubuntu2 [182 kB] 364s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libuuid1 ppc64el 2.39.3-9ubuntu2 [39.3 kB] 364s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcryptsetup12 ppc64el 2:2.7.0-1ubuntu2 [376 kB] 364s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfdisk1 ppc64el 2.39.3-9ubuntu2 [171 kB] 364s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libseccomp2 ppc64el 2.5.5-1ubuntu2 [62.5 kB] 364s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el mount ppc64el 2.39.3-9ubuntu2 [125 kB] 364s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmount1 ppc64el 2.39.3-9ubuntu2 [169 kB] 364s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el zlib1g ppc64el 1:1.3.dfsg-3.1ubuntu1 [72.8 kB] 364s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-minimal ppc64el 3.12.2-0ubuntu1 [27.1 kB] 364s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3 ppc64el 3.12.2-0ubuntu1 [24.1 kB] 364s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libplymouth5 ppc64el 24.004.60-1ubuntu6 [166 kB] 364s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpng16-16t64 ppc64el 1.6.43-3 [242 kB] 364s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbrotli1 ppc64el 1.1.0-2build1 [410 kB] 364s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfreetype6 ppc64el 2.13.2+dfsg-1build2 [545 kB] 364s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsqlite3-0 ppc64el 3.45.1-1ubuntu1 [804 kB] 364s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el pinentry-curses ppc64el 1.2.1-3ubuntu4 [38.7 kB] 364s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-14-base ppc64el 14-20240315-1ubuntu1 [47.0 kB] 364s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgcc-s1 ppc64el 14-20240315-1ubuntu1 [39.2 kB] 364s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libstdc++6 ppc64el 14-20240315-1ubuntu1 [897 kB] 364s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python-apt-common all 2.7.7 [19.8 kB] 364s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsmartcols1 ppc64el 2.39.3-9ubuntu2 [79.0 kB] 364s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el readline-common all 8.2-4 [56.4 kB] 364s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdextrautils ppc64el 2.39.3-9ubuntu2 [78.6 kB] 364s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el groff-base ppc64el 1.23.0-3build1 [1112 kB] 364s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.2-0ubuntu1 [9798 B] 364s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfido2-1 ppc64el 1.14.0-1build1 [111 kB] 364s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-6ubuntu1 [185 kB] 364s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5-3 ppc64el 1.20.1-6ubuntu1 [432 kB] 364s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5support0 ppc64el 1.20.1-6ubuntu1 [38.5 kB] 364s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libk5crypto3 ppc64el 1.20.1-6ubuntu1 [108 kB] 364s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcom-err2 ppc64el 1.47.0-2.4~exp1ubuntu2 [22.9 kB] 364s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libproc2-0 ppc64el 2:4.0.4-4ubuntu2 [68.8 kB] 364s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el procps ppc64el 2:4.0.4-4ubuntu2 [736 kB] 364s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnghttp2-14 ppc64el 1.59.0-1build1 [89.0 kB] 364s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg ppc64el 1.22.6ubuntu5 [1343 kB] 364s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el util-linux ppc64el 2.39.3-9ubuntu2 [1195 kB] 364s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.3ubuntu2 [840 kB] 364s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbpf1 ppc64el 1:1.3.0-2build1 [216 kB] 364s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el iproute2 ppc64el 6.1.0-1ubuntu5 [1384 kB] 364s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libelf1t64 ppc64el 0.190-1.1build2 [69.3 kB] 364s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dhcpcd-base ppc64el 1:10.0.6-1ubuntu2 [276 kB] 364s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el file ppc64el 1:5.45-3 [22.7 kB] 364s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmagic-mgc ppc64el 1:5.45-3 [307 kB] 364s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmagic1t64 ppc64el 1:5.45-3 [106 kB] 364s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc-common all 1.3.4+ds-1.1 [8018 B] 364s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el lsof ppc64el 4.95.0-1build2 [256 kB] 365s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnsl2 ppc64el 1.3.0-3build2 [48.9 kB] 365s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc3t64 ppc64el 1.3.4+ds-1.1 [102 kB] 365s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el multipath-tools ppc64el 0.9.4-5ubuntu6 [341 kB] 365s Get:207 http://ftpmaster.internal/ubuntu noble/main ppc64el liburcu8t64 ppc64el 0.14.0-3.1 [73.6 kB] 365s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bind9-host ppc64el 1:9.18.24-0ubuntu3 [54.5 kB] 365s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bind9-dnsutils ppc64el 1:9.18.24-0ubuntu3 [167 kB] 365s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bind9-libs ppc64el 1:9.18.24-0ubuntu3 [1436 kB] 365s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libuv1t64 ppc64el 1.48.0-1.1 [117 kB] 365s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblocale-gettext-perl ppc64el 1.07-6ubuntu4 [16.1 kB] 365s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el uuid-runtime ppc64el 2.39.3-9ubuntu2 [33.8 kB] 365s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdebconfclient0 ppc64el 0.271ubuntu2 [11.2 kB] 365s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsemanage-common all 3.5-1build4 [10.1 kB] 365s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsemanage2 ppc64el 3.5-1build4 [115 kB] 365s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el install-info ppc64el 7.1-3build1 [64.5 kB] 365s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13-base ppc64el 13.2.0-21ubuntu1 [48.3 kB] 365s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libss2 ppc64el 1.47.0-2.4~exp1ubuntu2 [18.0 kB] 365s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dmsetup ppc64el 2:1.02.185-3ubuntu2 [91.8 kB] 365s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el eject ppc64el 2.39.3-9ubuntu2 [28.2 kB] 365s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el krb5-locales all 1.20.1-6ubuntu1 [13.8 kB] 365s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 365s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libslang2 ppc64el 2.3.3-3build1 [501 kB] 365s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-charwidth-perl ppc64el 0.04-11build2 [9506 B] 365s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-iconv-perl ppc64el 1.7-8build2 [13.7 kB] 365s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-yaml ppc64el 6.0.1-2build1 [123 kB] 365s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-setuptools all 68.1.2-2ubuntu1 [396 kB] 365s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] 365s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el rsyslog ppc64el 8.2312.0-3ubuntu7 [629 kB] 365s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el vim-tiny ppc64el 2:9.1.0016-1ubuntu6 [1042 kB] 365s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el vim-common all 2:9.1.0016-1ubuntu6 [385 kB] 365s Get:233 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-user-dirs ppc64el 0.18-1 [20.0 kB] 365s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el xxd ppc64el 2:9.1.0016-1ubuntu6 [63.7 kB] 365s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el apparmor ppc64el 4.0.0-beta3-0ubuntu2 [747 kB] 365s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ftp all 20230507-2build1 [4724 B] 365s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el inetutils-telnet ppc64el 2:2.5-3ubuntu3 [115 kB] 365s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el info ppc64el 7.1-3build1 [188 kB] 365s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libusb-1.0-0 ppc64el 2:1.0.27-1 [64.0 kB] 365s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxmuu1 ppc64el 2:1.1.3-3build1 [9488 B] 365s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el lshw ppc64el 02.19.git.2021.06.19.996aaad9c7-2build2 [334 kB] 365s Get:242 http://ftpmaster.internal/ubuntu noble/main ppc64el manpages all 6.05.01-1 [1340 kB] 365s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el mtr-tiny ppc64el 0.95-1.1build1 [62.8 kB] 366s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el plymouth-theme-ubuntu-text ppc64el 24.004.60-1ubuntu6 [11.1 kB] 366s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el plymouth ppc64el 24.004.60-1ubuntu6 [155 kB] 366s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el telnet all 0.17+2.5-3ubuntu3 [3682 B] 366s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el usb.ids all 2024.03.18-1 [223 kB] 366s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el xz-utils ppc64el 5.6.0-0.2 [281 kB] 366s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libctf0 ppc64el 2.42-4ubuntu1 [112 kB] 366s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libctf-nobfd0 ppc64el 2.42-4ubuntu1 [112 kB] 366s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.42-4ubuntu1 [2473 kB] 366s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbinutils ppc64el 2.42-4ubuntu1 [699 kB] 366s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el binutils ppc64el 2.42-4ubuntu1 [3078 B] 366s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el binutils-common ppc64el 2.42-4ubuntu1 [217 kB] 366s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsframe1 ppc64el 2.42-4ubuntu1 [16.0 kB] 366s Get:256 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libllvm18 ppc64el 1:18.1.2-1ubuntu2 [28.9 MB] 368s Get:257 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libclang-cpp18 ppc64el 1:18.1.2-1ubuntu2 [14.6 MB] 369s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libbpfcc ppc64el 0.29.1+ds-1ubuntu4 [707 kB] 369s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-bpfcc all 0.29.1+ds-1ubuntu4 [40.2 kB] 369s Get:260 http://ftpmaster.internal/ubuntu noble/main ppc64el ieee-data all 20220827.1 [2113 kB] 369s Get:261 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-netaddr all 0.8.0-2ubuntu1 [319 kB] 369s Get:262 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el bpfcc-tools all 0.29.1+ds-1ubuntu4 [687 kB] 369s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libclang1-18 ppc64el 1:18.1.2-1ubuntu2 [8725 kB] 370s Get:264 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdw1t64 ppc64el 0.190-1.1build2 [301 kB] 370s Get:265 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el bpftrace ppc64el 0.20.2-1ubuntu1 [1058 kB] 370s Get:266 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el cryptsetup-bin ppc64el 2:2.7.0-1ubuntu2 [227 kB] 370s Get:267 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg-dev all 1.22.6ubuntu5 [1074 kB] 370s Get:268 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdpkg-perl all 1.22.6ubuntu5 [269 kB] 370s Get:269 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 370s Get:270 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 370s Get:271 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu1 [37.4 kB] 370s Get:272 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libprotobuf-c1 ppc64el 1.4.1-1ubuntu3 [25.9 kB] 370s Get:273 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB] 370s Get:274 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libibverbs1 ppc64el 50.0-2build1 [74.4 kB] 370s Get:275 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ibverbs-providers ppc64el 50.0-2build1 [420 kB] 370s Get:276 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el jq ppc64el 1.7.1-3 [66.1 kB] 370s Get:277 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjq1 ppc64el 1.7.1-3 [173 kB] 370s Get:278 http://ftpmaster.internal/ubuntu noble/main ppc64el libaio1t64 ppc64el 0.3.113-6 [8188 B] 370s Get:279 http://ftpmaster.internal/ubuntu noble/main ppc64el libatm1t64 ppc64el 1:2.5.1-5.1 [26.9 kB] 370s Get:280 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu6 [21.3 kB] 370s Get:281 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu1 [190 kB] 370s Get:282 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 370s Get:283 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 370s Get:284 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 370s Get:285 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 370s Get:286 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 370s Get:287 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4build2 [28.8 kB] 370s Get:288 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libwebp7 ppc64el 1.3.2-0.4build2 [312 kB] 370s Get:289 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu1 [274 kB] 370s Get:290 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxpm4 ppc64el 1:3.5.17-1build1 [50.2 kB] 370s Get:291 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgd3 ppc64el 2.3.3-9ubuntu3 [162 kB] 370s Get:292 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-devtools ppc64el 2.39-0ubuntu6 [29.6 kB] 370s Get:293 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-libc-dev ppc64el 6.8.0-20.20 [1586 kB] 370s Get:294 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 370s Get:295 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 370s Get:296 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu6 [2102 kB] 370s Get:297 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libevent-core-2.1-7 ppc64el 2.1.12-stable-9build1 [110 kB] 370s Get:298 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libftdi1-2 ppc64el 1.5-6build4 [32.5 kB] 370s Get:299 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB] 370s Get:300 http://ftpmaster.internal/ubuntu noble/main ppc64el libunwind8 ppc64el 1.6.2-3 [59.9 kB] 370s Get:301 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-modules-6.8.0-20-generic ppc64el 6.8.0-20.20 [31.3 MB] 373s Get:302 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-image-6.8.0-20-generic ppc64el 6.8.0-20.20 [63.9 MB] 378s Get:303 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-modules-extra-6.8.0-20-generic ppc64el 6.8.0-20.20 [103 MB] 385s Get:304 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-generic ppc64el 6.8.0-20.20+1 [1734 B] 385s Get:305 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-image-generic ppc64el 6.8.0-20.20+1 [9698 B] 385s Get:306 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-virtual ppc64el 6.8.0-20.20+1 [1686 B] 385s Get:307 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-image-virtual ppc64el 6.8.0-20.20+1 [9702 B] 385s Get:308 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-headers-virtual ppc64el 6.8.0-20.20+1 [1648 B] 385s Get:309 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB] 386s Get:310 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-headers-6.8.0-20-generic ppc64el 6.8.0-20.20 [3728 kB] 386s Get:311 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-headers-generic ppc64el 6.8.0-20.20+1 [9612 B] 386s Get:312 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-tools-common all 6.8.0-20.20 [437 kB] 386s Get:313 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-tools-6.8.0-20 ppc64el 6.8.0-20.20 [2924 kB] 386s Get:314 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-tools-6.8.0-20-generic ppc64el 6.8.0-20.20 [1730 B] 386s Get:315 http://ftpmaster.internal/ubuntu noble/main ppc64el manpages-dev all 6.05.01-1 [2018 kB] 386s Get:316 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-distutils all 3.12.2-3ubuntu1.1 [133 kB] 386s Get:317 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-lib2to3 all 3.12.2-3ubuntu1.1 [79.1 kB] 386s Get:318 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-pyrsistent ppc64el 0.20.0-1build1 [60.4 kB] 386s Get:319 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-typing-extensions all 4.10.0-1 [60.7 kB] 386s Get:320 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-kernel-accessories ppc64el 1.536build1 [10.5 kB] 386s Get:321 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el kpartx ppc64el 0.9.4-5ubuntu6 [34.4 kB] 387s Preconfiguring packages ... 387s Fetched 390 MB in 29s (13.4 MB/s) 387s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70153 files and directories currently installed.) 387s Preparing to unpack .../motd-news-config_13ubuntu8_all.deb ... 387s Unpacking motd-news-config (13ubuntu8) over (13ubuntu7) ... 387s Preparing to unpack .../base-files_13ubuntu8_ppc64el.deb ... 387s Unpacking base-files (13ubuntu8) over (13ubuntu7) ... 387s Setting up base-files (13ubuntu8) ... 388s motd-news.service is a disabled or a static unit not running, not starting it. 388s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70153 files and directories currently installed.) 388s Preparing to unpack .../bash_5.2.21-2ubuntu3_ppc64el.deb ... 388s Unpacking bash (5.2.21-2ubuntu3) over (5.2.21-2ubuntu2) ... 388s Setting up bash (5.2.21-2ubuntu3) ... 388s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 388s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70153 files and directories currently installed.) 388s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_ppc64el.deb ... 388s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ... 388s Setting up bsdutils (1:2.39.3-9ubuntu2) ... 388s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70153 files and directories currently installed.) 388s Preparing to unpack .../coreutils_9.4-3ubuntu3_ppc64el.deb ... 388s Unpacking coreutils (9.4-3ubuntu3) over (9.4-2ubuntu4) ... 388s Setting up coreutils (9.4-3ubuntu3) ... 388s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70153 files and directories currently installed.) 388s Preparing to unpack .../00-libudisks2-0_2.10.1-6_ppc64el.deb ... 388s Unpacking libudisks2-0:ppc64el (2.10.1-6) over (2.10.1-1ubuntu2) ... 388s Preparing to unpack .../01-udisks2_2.10.1-6_ppc64el.deb ... 388s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ... 388s Preparing to unpack .../02-shared-mime-info_2.4-1build1_ppc64el.deb ... 388s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ... 388s Preparing to unpack .../03-gir1.2-girepository-2.0_1.79.1-1ubuntu6_ppc64el.deb ... 388s Unpacking gir1.2-girepository-2.0:ppc64el (1.79.1-1ubuntu6) over (1.79.1-1) ... 388s Preparing to unpack .../04-gir1.2-glib-2.0_2.79.3-3ubuntu5_ppc64el.deb ... 388s Unpacking gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 388s Preparing to unpack .../05-libgirepository-1.0-1_1.79.1-1ubuntu6_ppc64el.deb ... 388s Unpacking libgirepository-1.0-1:ppc64el (1.79.1-1ubuntu6) over (1.79.1-1) ... 388s Preparing to unpack .../06-python3-gi_3.47.0-3build1_ppc64el.deb ... 388s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ... 388s Preparing to unpack .../07-python3-dbus_1.3.2-5build2_ppc64el.deb ... 389s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ... 389s Selecting previously unselected package libnetplan1:ppc64el. 389s Preparing to unpack .../08-libnetplan1_1.0-1_ppc64el.deb ... 389s Unpacking libnetplan1:ppc64el (1.0-1) ... 389s Preparing to unpack .../09-python3-netplan_1.0-1_ppc64el.deb ... 389s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ... 389s Preparing to unpack .../10-netplan-generator_1.0-1_ppc64el.deb ... 389s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 389s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ... 389s Preparing to unpack .../11-initramfs-tools-bin_0.142ubuntu23_ppc64el.deb ... 389s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ... 389s Preparing to unpack .../12-initramfs-tools-core_0.142ubuntu23_all.deb ... 389s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ... 389s Preparing to unpack .../13-initramfs-tools_0.142ubuntu23_all.deb ... 389s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ... 389s Preparing to unpack .../14-netplan.io_1.0-1_ppc64el.deb ... 389s Unpacking netplan.io (1.0-1) over (0.107.1-3) ... 389s Preparing to unpack .../15-libxmlb2_0.3.15-1build1_ppc64el.deb ... 389s Unpacking libxmlb2:ppc64el (0.3.15-1build1) over (0.3.15-1) ... 389s dpkg: libgpgme11:ppc64el: dependency problems, but removing anyway as you requested: 389s libvolume-key1:ppc64el depends on libgpgme11 (>= 1.4.1). 389s libjcat1:ppc64el depends on libgpgme11 (>= 1.2.0). 389s 389s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 389s Removing libgpgme11:ppc64el (1.18.0-4ubuntu1) ... 389s Selecting previously unselected package libgpgme11t64:ppc64el. 389s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70151 files and directories currently installed.) 389s Preparing to unpack .../00-libgpgme11t64_1.18.0-4.1ubuntu3_ppc64el.deb ... 389s Unpacking libgpgme11t64:ppc64el (1.18.0-4.1ubuntu3) ... 389s Preparing to unpack .../01-libvolume-key1_0.3.12-7build1_ppc64el.deb ... 389s Unpacking libvolume-key1:ppc64el (0.3.12-7build1) over (0.3.12-5build2) ... 389s Preparing to unpack .../02-libqrtr-glib0_1.2.2-1ubuntu3_ppc64el.deb ... 389s Unpacking libqrtr-glib0:ppc64el (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ... 389s Preparing to unpack .../03-libqmi-glib5_1.35.2-0ubuntu1_ppc64el.deb ... 389s Unpacking libqmi-glib5:ppc64el (1.35.2-0ubuntu1) over (1.34.0-2) ... 389s Preparing to unpack .../04-libqmi-proxy_1.35.2-0ubuntu1_ppc64el.deb ... 389s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ... 389s Preparing to unpack .../05-libpolkit-agent-1-0_124-1ubuntu1_ppc64el.deb ... 389s Unpacking libpolkit-agent-1-0:ppc64el (124-1ubuntu1) over (124-1) ... 389s Preparing to unpack .../06-libpolkit-gobject-1-0_124-1ubuntu1_ppc64el.deb ... 389s Unpacking libpolkit-gobject-1-0:ppc64el (124-1ubuntu1) over (124-1) ... 389s Preparing to unpack .../07-libmm-glib0_1.23.4-0ubuntu1_ppc64el.deb ... 389s Unpacking libmm-glib0:ppc64el (1.23.4-0ubuntu1) over (1.22.0-3) ... 389s Preparing to unpack .../08-libmbim-glib4_1.31.2-0ubuntu2_ppc64el.deb ... 389s Unpacking libmbim-glib4:ppc64el (1.31.2-0ubuntu2) over (1.30.0-1) ... 389s Preparing to unpack .../09-libmbim-proxy_1.31.2-0ubuntu2_ppc64el.deb ... 389s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ... 389s Preparing to unpack .../10-libjson-glib-1.0-common_1.8.0-2build1_all.deb ... 389s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ... 389s Preparing to unpack .../11-libjson-glib-1.0-0_1.8.0-2build1_ppc64el.deb ... 389s Unpacking libjson-glib-1.0-0:ppc64el (1.8.0-2build1) over (1.8.0-2) ... 389s Preparing to unpack .../12-libgusb2_0.4.8-1build1_ppc64el.deb ... 389s Unpacking libgusb2:ppc64el (0.4.8-1build1) over (0.4.8-1) ... 389s Preparing to unpack .../13-libgudev-1.0-0_1%3a238-3ubuntu2_ppc64el.deb ... 389s Unpacking libgudev-1.0-0:ppc64el (1:238-3ubuntu2) over (1:238-3) ... 389s Preparing to unpack .../14-tnftp_20230507-2build1_ppc64el.deb ... 389s Unpacking tnftp (20230507-2build1) over (20230507-2) ... 389s Preparing to unpack .../15-tcpdump_4.99.4-3ubuntu2_ppc64el.deb ... 389s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ... 389s Preparing to unpack .../16-libsystemd0_255.4-1ubuntu5_ppc64el.deb ... 389s Unpacking libsystemd0:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 389s Setting up libsystemd0:ppc64el (255.4-1ubuntu5) ... 389s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70158 files and directories currently installed.) 389s Preparing to unpack .../systemd-dev_255.4-1ubuntu5_all.deb ... 389s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 389s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_ppc64el.deb ... 389s Unpacking libnss-systemd:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 389s Preparing to unpack .../libudev1_255.4-1ubuntu5_ppc64el.deb ... 389s Unpacking libudev1:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 389s Setting up libudev1:ppc64el (255.4-1ubuntu5) ... 389s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 389s wget depends on libssl3 (>= 3.0.0). 389s systemd-resolved depends on libssl3 (>= 3.0.0). 389s systemd depends on libssl3 (>= 3.0.0). 389s sudo depends on libssl3 (>= 3.0.0). 389s rsync depends on libssl3 (>= 3.0.0). 389s python3-cryptography depends on libssl3 (>= 3.0.0). 389s openssl depends on libssl3 (>= 3.0.9). 389s openssh-server depends on libssl3 (>= 3.0.10). 389s openssh-client depends on libssl3 (>= 3.0.10). 389s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 389s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 389s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 389s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 389s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 389s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 389s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 389s libnvme1 depends on libssl3 (>= 3.0.0). 389s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 389s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 389s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 389s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 389s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 389s kmod depends on libssl3 (>= 3.0.0). 389s dhcpcd-base depends on libssl3 (>= 3.0.0). 389s coreutils depends on libssl3 (>= 3.0.0). 389s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 389s 389s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70158 files and directories currently installed.) 389s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 389s Selecting previously unselected package libssl3t64:ppc64el. 390s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70147 files and directories currently installed.) 390s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 390s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 390s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 390s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70160 files and directories currently installed.) 390s Preparing to unpack .../systemd_255.4-1ubuntu5_ppc64el.deb ... 390s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 390s Preparing to unpack .../udev_255.4-1ubuntu5_ppc64el.deb ... 390s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 390s Preparing to unpack .../libsystemd-shared_255.4-1ubuntu5_ppc64el.deb ... 390s Unpacking libsystemd-shared:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 390s Setting up libsystemd-shared:ppc64el (255.4-1ubuntu5) ... 390s Setting up systemd-dev (255.4-1ubuntu5) ... 390s Setting up systemd (255.4-1ubuntu5) ... 391s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70160 files and directories currently installed.) 391s Preparing to unpack .../00-systemd-sysv_255.4-1ubuntu5_ppc64el.deb ... 391s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 391s Preparing to unpack .../01-libpam-systemd_255.4-1ubuntu5_ppc64el.deb ... 391s Unpacking libpam-systemd:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 391s Preparing to unpack .../02-systemd-timesyncd_255.4-1ubuntu5_ppc64el.deb ... 391s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 391s Preparing to unpack .../03-systemd-resolved_255.4-1ubuntu5_ppc64el.deb ... 391s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 391s Preparing to unpack .../04-sudo_1.9.15p5-3ubuntu3_ppc64el.deb ... 391s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ... 391s Preparing to unpack .../05-rsync_3.2.7-1build1_ppc64el.deb ... 391s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ... 391s Preparing to unpack .../06-python3-cryptography_41.0.7-4build2_ppc64el.deb ... 391s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ... 391s Preparing to unpack .../07-openssl_3.0.13-0ubuntu2_ppc64el.deb ... 391s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 391s Preparing to unpack .../08-openssh-sftp-server_1%3a9.6p1-3ubuntu11_ppc64el.deb ... 391s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 391s Preparing to unpack .../09-openssh-client_1%3a9.6p1-3ubuntu11_ppc64el.deb ... 391s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 391s Preparing to unpack .../10-openssh-server_1%3a9.6p1-3ubuntu11_ppc64el.deb ... 392s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 392s Preparing to unpack .../11-libssh-4_0.10.6-2build1_ppc64el.deb ... 392s Unpacking libssh-4:ppc64el (0.10.6-2build1) over (0.10.6-2) ... 392s Preparing to unpack .../12-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_ppc64el.deb ... 392s Unpacking libsasl2-modules:ppc64el (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 392s Preparing to unpack .../13-python3.12_3.12.2-4build3_ppc64el.deb ... 392s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ... 392s Preparing to unpack .../14-python3.12-minimal_3.12.2-4build3_ppc64el.deb ... 392s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ... 392s Preparing to unpack .../15-libpython3.12-minimal_3.12.2-4build3_ppc64el.deb ... 392s Unpacking libpython3.12-minimal:ppc64el (3.12.2-4build3) over (3.12.2-1) ... 392s Preparing to unpack .../16-grub-ieee1275_2.12-1ubuntu5_ppc64el.deb ... 392s Unpacking grub-ieee1275 (2.12-1ubuntu5) over (2.12-1ubuntu4) ... 392s Preparing to unpack .../17-grub2-common_2.12-1ubuntu5_ppc64el.deb ... 392s Unpacking grub2-common (2.12-1ubuntu5) over (2.12-1ubuntu4) ... 392s Preparing to unpack .../18-grub-common_2.12-1ubuntu5_ppc64el.deb ... 392s Unpacking grub-common (2.12-1ubuntu5) over (2.12-1ubuntu4) ... 392s Preparing to unpack .../19-grub-ieee1275-bin_2.12-1ubuntu5_ppc64el.deb ... 392s Unpacking grub-ieee1275-bin (2.12-1ubuntu5) over (2.12-1ubuntu4) ... 392s dpkg: libparted2:ppc64el: dependency problems, but removing anyway as you requested: 392s parted depends on libparted2 (= 3.6-3). 392s 392s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70160 files and directories currently installed.) 392s Removing libparted2:ppc64el (3.6-3) ... 392s Selecting previously unselected package libparted2t64:ppc64el. 392s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70154 files and directories currently installed.) 392s Preparing to unpack .../0-libparted2t64_3.6-3.1build2_ppc64el.deb ... 392s Unpacking libparted2t64:ppc64el (3.6-3.1build2) ... 392s Preparing to unpack .../1-parted_3.6-3.1build2_ppc64el.deb ... 392s Unpacking parted (3.6-3.1build2) over (3.6-3) ... 392s Preparing to unpack .../2-python3.11_3.11.8-1build4_ppc64el.deb ... 392s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ... 392s Preparing to unpack .../3-python3.11-minimal_3.11.8-1build4_ppc64el.deb ... 392s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ... 393s Preparing to unpack .../4-libpython3.11-minimal_3.11.8-1build4_ppc64el.deb ... 393s Unpacking libpython3.11-minimal:ppc64el (3.11.8-1build4) over (3.11.8-1) ... 393s Preparing to unpack .../5-libpython3.11-stdlib_3.11.8-1build4_ppc64el.deb ... 393s Unpacking libpython3.11-stdlib:ppc64el (3.11.8-1build4) over (3.11.8-1) ... 393s Preparing to unpack .../6-gnupg-utils_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s Preparing to unpack .../7-gpg-agent_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s Preparing to unpack .../8-gpg-wks-client_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s Preparing to unpack .../9-gpg_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s dpkg: libnpth0:ppc64el: dependency problems, but removing anyway as you requested: 393s keyboxd depends on libnpth0 (>= 0.90). 393s gpgv depends on libnpth0 (>= 0.90). 393s gpgsm depends on libnpth0 (>= 0.90). 393s dirmngr depends on libnpth0 (>= 0.90). 393s 393s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70159 files and directories currently installed.) 393s Removing libnpth0:ppc64el (1.6-3build2) ... 393s Selecting previously unselected package libnpth0t64:ppc64el. 393s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70154 files and directories currently installed.) 393s Preparing to unpack .../libnpth0t64_1.6-3.1_ppc64el.deb ... 393s Unpacking libnpth0t64:ppc64el (1.6-3.1) ... 393s Setting up libnpth0t64:ppc64el (1.6-3.1) ... 393s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70160 files and directories currently installed.) 393s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s Setting up gpgv (2.4.4-2ubuntu15) ... 393s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70160 files and directories currently installed.) 393s Preparing to unpack .../dirmngr_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s Preparing to unpack .../gnupg_2.4.4-2ubuntu15_all.deb ... 393s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s Preparing to unpack .../gpgconf_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_ppc64el.deb ... 393s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 393s dpkg: libreadline8:ppc64el: dependency problems, but removing anyway as you requested: 393s libpython3.12-stdlib:ppc64el depends on libreadline8 (>= 7.0~beta). 393s gawk depends on libreadline8 (>= 6.0). 393s fdisk depends on libreadline8 (>= 6.0). 393s bc depends on libreadline8 (>= 6.0). 393s 393s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70160 files and directories currently installed.) 393s Removing libreadline8:ppc64el (8.2-3) ... 393s Selecting previously unselected package libreadline8t64:ppc64el. 393s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70148 files and directories currently installed.) 393s Preparing to unpack .../libreadline8t64_8.2-4_ppc64el.deb ... 393s Adding 'diversion of /lib/powerpc64le-linux-gnu/libhistory.so.8 to /lib/powerpc64le-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 393s Adding 'diversion of /lib/powerpc64le-linux-gnu/libhistory.so.8.2 to /lib/powerpc64le-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 393s Adding 'diversion of /lib/powerpc64le-linux-gnu/libreadline.so.8 to /lib/powerpc64le-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 393s Adding 'diversion of /lib/powerpc64le-linux-gnu/libreadline.so.8.2 to /lib/powerpc64le-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 393s Unpacking libreadline8t64:ppc64el (8.2-4) ... 393s Setting up libreadline8t64:ppc64el (8.2-4) ... 394s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70168 files and directories currently installed.) 394s Preparing to unpack .../gawk_1%3a5.2.1-2build2_ppc64el.deb ... 394s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ... 394s Preparing to unpack .../fdisk_2.39.3-9ubuntu2_ppc64el.deb ... 394s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 394s Preparing to unpack .../bc_1.07.1-3ubuntu2_ppc64el.deb ... 394s Unpacking bc (1.07.1-3ubuntu2) over (1.07.1-3build1) ... 394s Preparing to unpack .../libpython3.12-stdlib_3.12.2-4build3_ppc64el.deb ... 394s Unpacking libpython3.12-stdlib:ppc64el (3.12.2-4build3) over (3.12.2-1) ... 394s Preparing to unpack .../perl-base_5.38.2-3.2_ppc64el.deb ... 394s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 394s Setting up perl-base (5.38.2-3.2) ... 394s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70166 files and directories currently installed.) 394s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 394s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 394s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu1.1_ppc64el.deb ... 394s Unpacking python3-gdbm:ppc64el (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 395s Preparing to unpack .../man-db_2.12.0-3build4_ppc64el.deb ... 395s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ... 395s dpkg: libgdbm-compat4:ppc64el: dependency problems, but removing anyway as you requested: 395s libperl5.38:ppc64el depends on libgdbm-compat4 (>= 1.18-3). 395s 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70166 files and directories currently installed.) 395s Removing libgdbm-compat4:ppc64el (1.23-5) ... 395s dpkg: libgdbm6:ppc64el: dependency problems, but removing anyway as you requested: 395s libperl5.38:ppc64el depends on libgdbm6 (>= 1.21). 395s 395s Removing libgdbm6:ppc64el (1.23-5) ... 395s Selecting previously unselected package libgdbm6t64:ppc64el. 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70156 files and directories currently installed.) 395s Preparing to unpack .../libgdbm6t64_1.23-5.1_ppc64el.deb ... 395s Unpacking libgdbm6t64:ppc64el (1.23-5.1) ... 395s Selecting previously unselected package libgdbm-compat4t64:ppc64el. 395s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_ppc64el.deb ... 395s Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1) ... 395s dpkg: libperl5.38:ppc64el: dependency problems, but removing anyway as you requested: 395s perl depends on libperl5.38 (= 5.38.2-3). 395s 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70168 files and directories currently installed.) 395s Removing libperl5.38:ppc64el (5.38.2-3) ... 395s Selecting previously unselected package libperl5.38t64:ppc64el. 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69645 files and directories currently installed.) 395s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_ppc64el.deb ... 395s Unpacking libperl5.38t64:ppc64el (5.38.2-3.2) ... 395s Preparing to unpack .../perl_5.38.2-3.2_ppc64el.deb ... 395s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ... 395s dpkg: libdb5.3:ppc64el: dependency problems, but removing anyway as you requested: 395s libsasl2-modules-db:ppc64el depends on libdb5.3. 395s libpam-modules:ppc64el depends on libdb5.3. 395s iproute2 depends on libdb5.3. 395s apt-utils depends on libdb5.3. 395s 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70168 files and directories currently installed.) 395s Removing libdb5.3:ppc64el (5.3.28+dfsg2-4) ... 395s Selecting previously unselected package libdb5.3t64:ppc64el. 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70162 files and directories currently installed.) 395s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_ppc64el.deb ... 395s Unpacking libdb5.3t64:ppc64el (5.3.28+dfsg2-6) ... 395s Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_ppc64el.deb ... 395s Unpacking libsasl2-modules-db:ppc64el (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 395s Preparing to unpack .../libsasl2-2_2.1.28+dfsg1-5ubuntu1_ppc64el.deb ... 395s Unpacking libsasl2-2:ppc64el (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 395s dpkg: libnvme1: dependency problems, but removing anyway as you requested: 395s libblockdev-nvme3:ppc64el depends on libnvme1 (>= 1.7.1). 395s 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70168 files and directories currently installed.) 395s Removing libnvme1 (1.8-2) ... 395s Selecting previously unselected package libnvme1t64. 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70161 files and directories currently installed.) 395s Preparing to unpack .../libnvme1t64_1.8-3_ppc64el.deb ... 395s Unpacking libnvme1t64 (1.8-3) ... 395s Preparing to unpack .../wget_1.21.4-1ubuntu2_ppc64el.deb ... 395s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ... 395s dpkg: libcurl4:ppc64el: dependency problems, but removing anyway as you requested: 395s curl depends on libcurl4 (= 8.5.0-2ubuntu2). 395s 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70169 files and directories currently installed.) 395s Removing libcurl4:ppc64el (8.5.0-2ubuntu2) ... 395s Selecting previously unselected package libcurl4t64:ppc64el. 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70164 files and directories currently installed.) 396s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu8_ppc64el.deb ... 396s Unpacking libcurl4t64:ppc64el (8.5.0-2ubuntu8) ... 396s Preparing to unpack .../curl_8.5.0-2ubuntu8_ppc64el.deb ... 396s Unpacking curl (8.5.0-2ubuntu8) over (8.5.0-2ubuntu2) ... 396s dpkg: libpsl5:ppc64el: dependency problems, but removing anyway as you requested: 396s libcurl3-gnutls:ppc64el depends on libpsl5 (>= 0.16.0). 396s 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70170 files and directories currently installed.) 396s Removing libpsl5:ppc64el (0.21.2-1build1) ... 396s Selecting previously unselected package libpsl5t64:ppc64el. 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70165 files and directories currently installed.) 396s Preparing to unpack .../libpsl5t64_0.21.2-1.1_ppc64el.deb ... 396s Unpacking libpsl5t64:ppc64el (0.21.2-1.1) ... 396s dpkg: libarchive13:ppc64el: dependency problems, but removing anyway as you requested: 396s fwupd depends on libarchive13 (>= 3.2.1). 396s 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70171 files and directories currently installed.) 396s Removing libarchive13:ppc64el (3.7.2-1ubuntu2) ... 396s Selecting previously unselected package libarchive13t64:ppc64el. 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70165 files and directories currently installed.) 396s Preparing to unpack .../libarchive13t64_3.7.2-1.1ubuntu2_ppc64el.deb ... 396s Unpacking libarchive13t64:ppc64el (3.7.2-1.1ubuntu2) ... 396s Preparing to unpack .../fwupd_1.9.15-2_ppc64el.deb ... 396s Unpacking fwupd (1.9.15-2) over (1.9.14-1) ... 396s dpkg: libcurl3-gnutls:ppc64el: dependency problems, but removing anyway as you requested: 396s libfwupd2:ppc64el depends on libcurl3-gnutls (>= 7.63.0). 396s 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70172 files and directories currently installed.) 396s Removing libcurl3-gnutls:ppc64el (8.5.0-2ubuntu2) ... 396s Selecting previously unselected package libcurl3t64-gnutls:ppc64el. 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70165 files and directories currently installed.) 396s Preparing to unpack .../00-libcurl3t64-gnutls_8.5.0-2ubuntu8_ppc64el.deb ... 396s Unpacking libcurl3t64-gnutls:ppc64el (8.5.0-2ubuntu8) ... 396s Preparing to unpack .../01-libfwupd2_1.9.15-2_ppc64el.deb ... 396s Unpacking libfwupd2:ppc64el (1.9.15-2) over (1.9.14-1) ... 396s Preparing to unpack .../02-libblockdev3_3.1.0-1build1_ppc64el.deb ... 396s Unpacking libblockdev3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 396s Preparing to unpack .../03-libblockdev-utils3_3.1.0-1build1_ppc64el.deb ... 396s Unpacking libblockdev-utils3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 396s Preparing to unpack .../04-libblockdev-swap3_3.1.0-1build1_ppc64el.deb ... 396s Unpacking libblockdev-swap3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 396s Preparing to unpack .../05-libblockdev-part3_3.1.0-1build1_ppc64el.deb ... 396s Unpacking libblockdev-part3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 396s Preparing to unpack .../06-libblockdev-nvme3_3.1.0-1build1_ppc64el.deb ... 396s Unpacking libblockdev-nvme3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 396s Preparing to unpack .../07-libblockdev-mdraid3_3.1.0-1build1_ppc64el.deb ... 396s Unpacking libblockdev-mdraid3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 396s Preparing to unpack .../08-libblockdev-loop3_3.1.0-1build1_ppc64el.deb ... 396s Unpacking libblockdev-loop3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 396s Preparing to unpack .../09-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ... 396s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 396s Preparing to unpack .../10-logsave_1.47.0-2.4~exp1ubuntu2_ppc64el.deb ... 396s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 396s dpkg: libext2fs2:ppc64el: dependency problems, but removing anyway as you requested: 396s libblockdev-fs3:ppc64el depends on libext2fs2 (>= 1.42.11). 396s e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). 396s btrfs-progs depends on libext2fs2 (>= 1.42). 396s 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70172 files and directories currently installed.) 396s Removing libext2fs2:ppc64el (1.47.0-2ubuntu1) ... 396s Selecting previously unselected package libext2fs2t64:ppc64el. 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70165 files and directories currently installed.) 396s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_ppc64el.deb ... 396s Adding 'diversion of /lib/powerpc64le-linux-gnu/libe2p.so.2 to /lib/powerpc64le-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' 396s Adding 'diversion of /lib/powerpc64le-linux-gnu/libe2p.so.2.3 to /lib/powerpc64le-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' 396s Adding 'diversion of /lib/powerpc64le-linux-gnu/libext2fs.so.2 to /lib/powerpc64le-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' 396s Adding 'diversion of /lib/powerpc64le-linux-gnu/libext2fs.so.2.4 to /lib/powerpc64le-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' 396s Unpacking libext2fs2t64:ppc64el (1.47.0-2.4~exp1ubuntu2) ... 396s Setting up libext2fs2t64:ppc64el (1.47.0-2.4~exp1ubuntu2) ... 396s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70181 files and directories currently installed.) 396s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_ppc64el.deb ... 396s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 397s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested: 397s btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27). 397s 397s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70181 files and directories currently installed.) 397s Removing libreiserfscore0 (1:3.6.27-7) ... 397s Selecting previously unselected package libreiserfscore0t64. 397s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70176 files and directories currently installed.) 397s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_ppc64el.deb ... 397s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ... 397s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_ppc64el.deb ... 397s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ... 397s Preparing to unpack .../libblockdev-fs3_3.1.0-1build1_ppc64el.deb ... 397s Unpacking libblockdev-fs3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 397s Preparing to unpack .../libblockdev-crypto3_3.1.0-1build1_ppc64el.deb ... 397s Unpacking libblockdev-crypto3:ppc64el (3.1.0-1build1) over (3.1.0-1) ... 397s Preparing to unpack .../bolt_0.9.6-2build1_ppc64el.deb ... 397s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ... 397s dpkg: libglib2.0-0:ppc64el: dependency problems, but removing anyway as you requested: 397s libnetplan0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 397s libjcat1:ppc64el depends on libglib2.0-0 (>= 2.75.3). 397s 397s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70182 files and directories currently installed.) 397s Removing libglib2.0-0:ppc64el (2.79.2-1~ubuntu1) ... 397s Selecting previously unselected package libglib2.0-0t64:ppc64el. 397s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 397s Preparing to unpack .../0-libglib2.0-0t64_2.79.3-3ubuntu5_ppc64el.deb ... 397s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 397s removed '/var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm' 397s Unpacking libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 397s Preparing to unpack .../1-libjcat1_0.2.0-2build2_ppc64el.deb ... 397s Unpacking libjcat1:ppc64el (0.2.0-2build2) over (0.2.0-2) ... 397s Preparing to unpack .../2-libldap2_2.6.7+dfsg-1~exp1ubuntu6_ppc64el.deb ... 397s Unpacking libldap2:ppc64el (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 397s Preparing to unpack .../3-ubuntu-pro-client-l10n_31.2.2_ppc64el.deb ... 397s Unpacking ubuntu-pro-client-l10n (31.2.2) over (31.1) ... 397s Preparing to unpack .../4-ubuntu-pro-client_31.2.2_ppc64el.deb ... 397s Unpacking ubuntu-pro-client (31.2.2) over (31.1) ... 397s Preparing to unpack .../5-python3-apt_2.7.7_ppc64el.deb ... 398s Unpacking python3-apt (2.7.7) over (2.7.6) ... 398s Preparing to unpack .../6-apt-utils_2.7.14_ppc64el.deb ... 398s Unpacking apt-utils (2.7.14) over (2.7.12) ... 398s dpkg: libapt-pkg6.0:ppc64el: dependency problems, but removing anyway as you requested: 398s apt depends on libapt-pkg6.0 (>= 2.7.12). 398s 398s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70180 files and directories currently installed.) 398s Removing libapt-pkg6.0:ppc64el (2.7.12) ... 398s dpkg: libnettle8:ppc64el: dependency problems, but removing anyway as you requested: 398s librtmp1:ppc64el depends on libnettle8. 398s libhogweed6:ppc64el depends on libnettle8. 398s libgnutls30:ppc64el depends on libnettle8 (>= 3.9~). 398s 398s Removing libnettle8:ppc64el (3.9.1-2) ... 398s Selecting previously unselected package libapt-pkg6.0t64:ppc64el. 398s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70124 files and directories currently installed.) 398s Preparing to unpack .../libapt-pkg6.0t64_2.7.14_ppc64el.deb ... 398s Unpacking libapt-pkg6.0t64:ppc64el (2.7.14) ... 398s Setting up libapt-pkg6.0t64:ppc64el (2.7.14) ... 398s Selecting previously unselected package libnettle8t64:ppc64el. 398s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70174 files and directories currently installed.) 398s Preparing to unpack .../libnettle8t64_3.9.1-2.2_ppc64el.deb ... 398s Unpacking libnettle8t64:ppc64el (3.9.1-2.2) ... 398s Setting up libnettle8t64:ppc64el (3.9.1-2.2) ... 398s dpkg: libhogweed6:ppc64el: dependency problems, but removing anyway as you requested: 398s librtmp1:ppc64el depends on libhogweed6. 398s libgnutls30:ppc64el depends on libhogweed6 (>= 3.6). 398s 398s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70182 files and directories currently installed.) 398s Removing libhogweed6:ppc64el (3.9.1-2) ... 398s Selecting previously unselected package libhogweed6t64:ppc64el. 398s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70177 files and directories currently installed.) 398s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_ppc64el.deb ... 398s Unpacking libhogweed6t64:ppc64el (3.9.1-2.2) ... 398s Setting up libhogweed6t64:ppc64el (3.9.1-2.2) ... 398s dpkg: libgnutls30:ppc64el: dependency problems, but removing anyway as you requested: 398s librtmp1:ppc64el depends on libgnutls30 (>= 3.7.2). 398s apt depends on libgnutls30 (>= 3.8.1). 398s 398s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70183 files and directories currently installed.) 398s Removing libgnutls30:ppc64el (3.8.3-1ubuntu1) ... 398s Selecting previously unselected package libgnutls30t64:ppc64el. 398s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70174 files and directories currently installed.) 398s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_ppc64el.deb ... 398s Unpacking libgnutls30t64:ppc64el (3.8.3-1.1ubuntu2) ... 398s Setting up libgnutls30t64:ppc64el (3.8.3-1.1ubuntu2) ... 398s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 398s Preparing to unpack .../apt_2.7.14_ppc64el.deb ... 398s Unpacking apt (2.7.14) over (2.7.12) ... 398s Setting up apt (2.7.14) ... 399s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 399s Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2build6_ppc64el.deb ... 399s Unpacking librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ... 399s Preparing to unpack .../liblzma5_5.6.0-0.2_ppc64el.deb ... 399s Unpacking liblzma5:ppc64el (5.6.0-0.2) over (5.4.5-0.3) ... 399s Setting up liblzma5:ppc64el (5.6.0-0.2) ... 399s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 399s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_ppc64el.deb ... 399s Unpacking libblkid1:ppc64el (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 399s Setting up libblkid1:ppc64el (2.39.3-9ubuntu2) ... 399s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 399s Preparing to unpack .../kmod_31+20240202-2ubuntu4_ppc64el.deb ... 399s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 399s Preparing to unpack .../libkmod2_31+20240202-2ubuntu4_ppc64el.deb ... 399s Unpacking libkmod2:ppc64el (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 399s Preparing to unpack .../libselinux1_3.5-2ubuntu1_ppc64el.deb ... 399s Unpacking libselinux1:ppc64el (3.5-2ubuntu1) over (3.5-2build1) ... 399s Setting up libselinux1:ppc64el (3.5-2ubuntu1) ... 399s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 399s Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ... 399s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ... 399s Setting up libaudit-common (1:3.1.2-2.1) ... 399s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 399s Preparing to unpack .../libcap-ng0_0.8.4-2build1_ppc64el.deb ... 399s Unpacking libcap-ng0:ppc64el (0.8.4-2build1) over (0.8.4-2) ... 399s Setting up libcap-ng0:ppc64el (0.8.4-2build1) ... 399s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 399s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_ppc64el.deb ... 399s Unpacking libaudit1:ppc64el (1:3.1.2-2.1) over (1:3.1.2-2) ... 399s Setting up libaudit1:ppc64el (1:3.1.2-2.1) ... 400s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 400s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_ppc64el.deb ... 400s Unpacking libpam0g:ppc64el (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 400s Setting up libpam0g:ppc64el (1.5.3-5ubuntu3) ... 400s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 400s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_ppc64el.deb ... 400s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 400s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ... 400s pam_namespace.service is a disabled or a static unit not running, not starting it. 400s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 400s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_ppc64el.deb ... 400s Unpacking libpam-modules:ppc64el (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 400s Setting up libpam-modules:ppc64el (1.5.3-5ubuntu3) ... 400s Installing new version of config file /etc/security/namespace.init ... 400s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70200 files and directories currently installed.) 400s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu3_all.deb ... 400s Unpacking libpam-runtime (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 400s Setting up libpam-runtime (1.5.3-5ubuntu3) ... 401s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70200 files and directories currently installed.) 401s Preparing to unpack .../00-dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ... 401s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 401s Preparing to unpack .../01-dbus-user-session_1.14.10-4ubuntu2_ppc64el.deb ... 401s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 401s Preparing to unpack .../02-libapparmor1_4.0.0-beta3-0ubuntu2_ppc64el.deb ... 401s Unpacking libapparmor1:ppc64el (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 401s Preparing to unpack .../03-libexpat1_2.6.1-2_ppc64el.deb ... 401s Unpacking libexpat1:ppc64el (2.6.1-2) over (2.6.0-1) ... 401s Preparing to unpack .../04-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ... 401s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 401s Preparing to unpack .../05-dbus-bin_1.14.10-4ubuntu2_ppc64el.deb ... 401s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 401s Preparing to unpack .../06-dbus_1.14.10-4ubuntu2_ppc64el.deb ... 401s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 401s Preparing to unpack .../07-dbus-daemon_1.14.10-4ubuntu2_ppc64el.deb ... 401s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 401s Preparing to unpack .../08-libdbus-1-3_1.14.10-4ubuntu2_ppc64el.deb ... 401s Unpacking libdbus-1-3:ppc64el (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 401s Preparing to unpack .../09-libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_ppc64el.deb ... 401s Unpacking libdevmapper1.02.1:ppc64el (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 401s Preparing to unpack .../10-libuuid1_2.39.3-9ubuntu2_ppc64el.deb ... 401s Unpacking libuuid1:ppc64el (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 401s Setting up libuuid1:ppc64el (2.39.3-9ubuntu2) ... 401s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70200 files and directories currently installed.) 402s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_ppc64el.deb ... 402s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 402s Setting up python3-minimal (3.12.2-0ubuntu1) ... 402s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70200 files and directories currently installed.) 402s Preparing to unpack .../python3_3.12.2-0ubuntu1_ppc64el.deb ... 403s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 403s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu6_ppc64el.deb ... 403s Unpacking libplymouth5:ppc64el (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 403s dpkg: libpng16-16:ppc64el: dependency problems, but removing anyway as you requested: 403s libfreetype6:ppc64el depends on libpng16-16 (>= 1.6.2-1). 403s 403s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70200 files and directories currently installed.) 403s Removing libpng16-16:ppc64el (1.6.43-1) ... 403s Selecting previously unselected package libpng16-16t64:ppc64el. 403s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70190 files and directories currently installed.) 403s Preparing to unpack .../0-libpng16-16t64_1.6.43-3_ppc64el.deb ... 403s Unpacking libpng16-16t64:ppc64el (1.6.43-3) ... 403s Preparing to unpack .../1-libbrotli1_1.1.0-2build1_ppc64el.deb ... 403s Unpacking libbrotli1:ppc64el (1.1.0-2build1) over (1.1.0-2) ... 403s Preparing to unpack .../2-libfreetype6_2.13.2+dfsg-1build2_ppc64el.deb ... 403s Unpacking libfreetype6:ppc64el (2.13.2+dfsg-1build2) over (2.13.2+dfsg-1) ... 403s Preparing to unpack .../3-libsqlite3-0_3.45.1-1ubuntu1_ppc64el.deb ... 403s Unpacking libsqlite3-0:ppc64el (3.45.1-1ubuntu1) over (3.45.1-1) ... 403s Preparing to unpack .../4-pinentry-curses_1.2.1-3ubuntu4_ppc64el.deb ... 403s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ... 403s Preparing to unpack .../5-gcc-14-base_14-20240315-1ubuntu1_ppc64el.deb ... 403s Unpacking gcc-14-base:ppc64el (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 403s Setting up gcc-14-base:ppc64el (14-20240315-1ubuntu1) ... 403s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70201 files and directories currently installed.) 403s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_ppc64el.deb ... 403s Unpacking libgcc-s1:ppc64el (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 403s Setting up libgcc-s1:ppc64el (14-20240315-1ubuntu1) ... 403s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70201 files and directories currently installed.) 403s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_ppc64el.deb ... 403s Unpacking libstdc++6:ppc64el (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 403s Setting up libstdc++6:ppc64el (14-20240315-1ubuntu1) ... 403s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70201 files and directories currently installed.) 403s Preparing to unpack .../python-apt-common_2.7.7_all.deb ... 403s Unpacking python-apt-common (2.7.7) over (2.7.6) ... 403s Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu2_ppc64el.deb ... 403s Unpacking libsmartcols1:ppc64el (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 403s Setting up libsmartcols1:ppc64el (2.39.3-9ubuntu2) ... 403s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70201 files and directories currently installed.) 403s Preparing to unpack .../00-readline-common_8.2-4_all.deb ... 403s Unpacking readline-common (8.2-4) over (8.2-3) ... 403s Preparing to unpack .../01-bsdextrautils_2.39.3-9ubuntu2_ppc64el.deb ... 403s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 403s Preparing to unpack .../02-groff-base_1.23.0-3build1_ppc64el.deb ... 403s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ... 403s Preparing to unpack .../03-libpython3-stdlib_3.12.2-0ubuntu1_ppc64el.deb ... 403s Unpacking libpython3-stdlib:ppc64el (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 403s Preparing to unpack .../04-libfido2-1_1.14.0-1build1_ppc64el.deb ... 403s Unpacking libfido2-1:ppc64el (1.14.0-1build1) over (1.14.0-1) ... 403s Preparing to unpack .../05-libgssapi-krb5-2_1.20.1-6ubuntu1_ppc64el.deb ... 403s Unpacking libgssapi-krb5-2:ppc64el (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 403s Preparing to unpack .../06-libkrb5-3_1.20.1-6ubuntu1_ppc64el.deb ... 403s Unpacking libkrb5-3:ppc64el (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 403s Preparing to unpack .../07-libkrb5support0_1.20.1-6ubuntu1_ppc64el.deb ... 403s Unpacking libkrb5support0:ppc64el (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 403s Preparing to unpack .../08-libk5crypto3_1.20.1-6ubuntu1_ppc64el.deb ... 403s Unpacking libk5crypto3:ppc64el (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 403s Preparing to unpack .../09-libcom-err2_1.47.0-2.4~exp1ubuntu2_ppc64el.deb ... 403s Unpacking libcom-err2:ppc64el (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 403s Preparing to unpack .../10-libproc2-0_2%3a4.0.4-4ubuntu2_ppc64el.deb ... 403s Unpacking libproc2-0:ppc64el (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 403s Preparing to unpack .../11-procps_2%3a4.0.4-4ubuntu2_ppc64el.deb ... 403s Unpacking procps (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 403s Preparing to unpack .../12-libnghttp2-14_1.59.0-1build1_ppc64el.deb ... 403s Unpacking libnghttp2-14:ppc64el (1.59.0-1build1) over (1.59.0-1) ... 403s Preparing to unpack .../13-dpkg_1.22.6ubuntu5_ppc64el.deb ... 404s Unpacking dpkg (1.22.6ubuntu5) over (1.22.4ubuntu5) ... 404s Setting up dpkg (1.22.6ubuntu5) ... 404s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 404s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_ppc64el.deb ... 404s Unpacking util-linux (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 404s Setting up util-linux (2.39.3-9ubuntu2) ... 405s fstrim.service is a disabled or a static unit not running, not starting it. 405s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 405s Preparing to unpack .../libxml2_2.9.14+dfsg-1.3ubuntu2_ppc64el.deb ... 405s Unpacking libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ... 405s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 405s Removing libatm1:ppc64el (1:2.5.1-5) ... 405s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70197 files and directories currently installed.) 405s Preparing to unpack .../libbpf1_1%3a1.3.0-2build1_ppc64el.deb ... 405s Unpacking libbpf1:ppc64el (1:1.3.0-2build1) over (1:1.3.0-2) ... 405s Preparing to unpack .../iproute2_6.1.0-1ubuntu5_ppc64el.deb ... 405s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ... 405s dpkg: libelf1:ppc64el: dependency problems, but removing anyway as you requested: 405s linux-headers-6.8.0-11-generic depends on libelf1 (>= 0.144). 405s 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70197 files and directories currently installed.) 406s Removing libelf1:ppc64el (0.190-1) ... 406s Selecting previously unselected package libelf1t64:ppc64el. 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70192 files and directories currently installed.) 406s Preparing to unpack .../libelf1t64_0.190-1.1build2_ppc64el.deb ... 406s Unpacking libelf1t64:ppc64el (0.190-1.1build2) ... 406s Preparing to unpack .../dhcpcd-base_1%3a10.0.6-1ubuntu2_ppc64el.deb ... 406s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ... 406s Preparing to unpack .../file_1%3a5.45-3_ppc64el.deb ... 406s Unpacking file (1:5.45-3) over (1:5.45-2) ... 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70197 files and directories currently installed.) 406s Removing libmagic1:ppc64el (1:5.45-2) ... 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70187 files and directories currently installed.) 406s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_ppc64el.deb ... 406s Unpacking libmagic-mgc (1:5.45-3) over (1:5.45-2) ... 406s Selecting previously unselected package libmagic1t64:ppc64el. 406s Preparing to unpack .../libmagic1t64_1%3a5.45-3_ppc64el.deb ... 406s Unpacking libmagic1t64:ppc64el (1:5.45-3) ... 406s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 406s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 406s Preparing to unpack .../lsof_4.95.0-1build2_ppc64el.deb ... 406s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ... 406s Preparing to unpack .../libnsl2_1.3.0-3build2_ppc64el.deb ... 406s Unpacking libnsl2:ppc64el (1.3.0-3build2) over (1.3.0-3) ... 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70198 files and directories currently installed.) 406s Removing libtirpc3:ppc64el (1.3.4+ds-1build1) ... 406s Selecting previously unselected package libtirpc3t64:ppc64el. 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70192 files and directories currently installed.) 406s Preparing to unpack .../libtirpc3t64_1.3.4+ds-1.1_ppc64el.deb ... 406s Adding 'diversion of /lib/powerpc64le-linux-gnu/libtirpc.so.3 to /lib/powerpc64le-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 406s Adding 'diversion of /lib/powerpc64le-linux-gnu/libtirpc.so.3.0.0 to /lib/powerpc64le-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 406s Unpacking libtirpc3t64:ppc64el (1.3.4+ds-1.1) ... 406s Preparing to unpack .../multipath-tools_0.9.4-5ubuntu6_ppc64el.deb ... 406s Unpacking multipath-tools (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ... 406s dpkg: liburcu8:ppc64el: dependency problems, but removing anyway as you requested: 406s xfsprogs depends on liburcu8 (>= 0.13.0). 406s 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70202 files and directories currently installed.) 406s Removing liburcu8:ppc64el (0.14.0-3) ... 406s Selecting previously unselected package liburcu8t64:ppc64el. 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70183 files and directories currently installed.) 406s Preparing to unpack .../liburcu8t64_0.14.0-3.1_ppc64el.deb ... 406s Unpacking liburcu8t64:ppc64el (0.14.0-3.1) ... 406s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_ppc64el.deb ... 406s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 406s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_ppc64el.deb ... 406s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 406s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_ppc64el.deb ... 406s Unpacking bind9-libs:ppc64el (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70203 files and directories currently installed.) 406s Removing libuv1:ppc64el (1.48.0-1) ... 406s Selecting previously unselected package libuv1t64:ppc64el. 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70198 files and directories currently installed.) 406s Preparing to unpack .../libuv1t64_1.48.0-1.1_ppc64el.deb ... 406s Unpacking libuv1t64:ppc64el (1.48.0-1.1) ... 406s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu4_ppc64el.deb ... 406s Unpacking liblocale-gettext-perl (1.07-6ubuntu4) over (1.07-6build1) ... 406s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_ppc64el.deb ... 406s Unpacking uuid-runtime (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 406s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_ppc64el.deb ... 406s Unpacking libdebconfclient0:ppc64el (0.271ubuntu2) over (0.271ubuntu1) ... 406s Setting up libdebconfclient0:ppc64el (0.271ubuntu2) ... 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70204 files and directories currently installed.) 406s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ... 406s Unpacking libsemanage-common (3.5-1build4) over (3.5-1build2) ... 406s Setting up libsemanage-common (3.5-1build4) ... 406s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70204 files and directories currently installed.) 406s Preparing to unpack .../libsemanage2_3.5-1build4_ppc64el.deb ... 406s Unpacking libsemanage2:ppc64el (3.5-1build4) over (3.5-1build2) ... 407s Setting up libsemanage2:ppc64el (3.5-1build4) ... 407s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70204 files and directories currently installed.) 407s Preparing to unpack .../install-info_7.1-3build1_ppc64el.deb ... 407s Unpacking install-info (7.1-3build1) over (7.1-3) ... 407s Setting up install-info (7.1-3build1) ... 407s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70204 files and directories currently installed.) 407s Preparing to unpack .../000-gcc-13-base_13.2.0-21ubuntu1_ppc64el.deb ... 407s Unpacking gcc-13-base:ppc64el (13.2.0-21ubuntu1) over (13.2.0-17ubuntu2) ... 407s Preparing to unpack .../001-libss2_1.47.0-2.4~exp1ubuntu2_ppc64el.deb ... 407s Unpacking libss2:ppc64el (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 407s Preparing to unpack .../002-dmsetup_2%3a1.02.185-3ubuntu2_ppc64el.deb ... 407s Unpacking dmsetup (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 407s Preparing to unpack .../003-eject_2.39.3-9ubuntu2_ppc64el.deb ... 407s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 407s Preparing to unpack .../004-krb5-locales_1.20.1-6ubuntu1_all.deb ... 407s Unpacking krb5-locales (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 407s Preparing to unpack .../005-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 407s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 407s Preparing to unpack .../006-libslang2_2.3.3-3build1_ppc64el.deb ... 407s Unpacking libslang2:ppc64el (2.3.3-3build1) over (2.3.3-3) ... 407s Preparing to unpack .../007-libtext-charwidth-perl_0.04-11build2_ppc64el.deb ... 407s Unpacking libtext-charwidth-perl:ppc64el (0.04-11build2) over (0.04-11build1) ... 407s Preparing to unpack .../008-libtext-iconv-perl_1.7-8build2_ppc64el.deb ... 407s Unpacking libtext-iconv-perl:ppc64el (1.7-8build2) over (1.7-8build1) ... 407s Preparing to unpack .../009-python3-yaml_6.0.1-2build1_ppc64el.deb ... 407s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ... 407s Preparing to unpack .../010-python3-setuptools_68.1.2-2ubuntu1_all.deb ... 407s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ... 407s Preparing to unpack .../011-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ... 407s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ... 407s Preparing to unpack .../012-rsyslog_8.2312.0-3ubuntu7_ppc64el.deb ... 407s Unpacking rsyslog (8.2312.0-3ubuntu7) over (8.2312.0-3ubuntu3) ... 407s Preparing to unpack .../013-vim-tiny_2%3a9.1.0016-1ubuntu6_ppc64el.deb ... 407s Unpacking vim-tiny (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ... 407s Preparing to unpack .../014-vim-common_2%3a9.1.0016-1ubuntu6_all.deb ... 407s Unpacking vim-common (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ... 407s Selecting previously unselected package xdg-user-dirs. 407s Preparing to unpack .../015-xdg-user-dirs_0.18-1_ppc64el.deb ... 407s Unpacking xdg-user-dirs (0.18-1) ... 407s Preparing to unpack .../016-xxd_2%3a9.1.0016-1ubuntu6_ppc64el.deb ... 407s Unpacking xxd (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ... 407s Preparing to unpack .../017-apparmor_4.0.0-beta3-0ubuntu2_ppc64el.deb ... 408s Unpacking apparmor (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 408s Preparing to unpack .../018-ftp_20230507-2build1_all.deb ... 408s Unpacking ftp (20230507-2build1) over (20230507-2) ... 408s Preparing to unpack .../019-inetutils-telnet_2%3a2.5-3ubuntu3_ppc64el.deb ... 408s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ... 408s Preparing to unpack .../020-info_7.1-3build1_ppc64el.deb ... 408s Unpacking info (7.1-3build1) over (7.1-3) ... 408s Preparing to unpack .../021-libusb-1.0-0_2%3a1.0.27-1_ppc64el.deb ... 408s Unpacking libusb-1.0-0:ppc64el (2:1.0.27-1) over (2:1.0.26-1) ... 408s Preparing to unpack .../022-libxmuu1_2%3a1.1.3-3build1_ppc64el.deb ... 408s Unpacking libxmuu1:ppc64el (2:1.1.3-3build1) over (2:1.1.3-3) ... 408s Preparing to unpack .../023-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_ppc64el.deb ... 408s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ... 408s Selecting previously unselected package manpages. 408s Preparing to unpack .../024-manpages_6.05.01-1_all.deb ... 408s Unpacking manpages (6.05.01-1) ... 408s Preparing to unpack .../025-mtr-tiny_0.95-1.1build1_ppc64el.deb ... 408s Unpacking mtr-tiny (0.95-1.1build1) over (0.95-1.1) ... 408s Preparing to unpack .../026-plymouth-theme-ubuntu-text_24.004.60-1ubuntu6_ppc64el.deb ... 408s Unpacking plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 408s Preparing to unpack .../027-plymouth_24.004.60-1ubuntu6_ppc64el.deb ... 408s Unpacking plymouth (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 408s Preparing to unpack .../028-telnet_0.17+2.5-3ubuntu3_all.deb ... 408s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ... 408s Preparing to unpack .../029-usb.ids_2024.03.18-1_all.deb ... 408s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ... 408s Preparing to unpack .../030-xz-utils_5.6.0-0.2_ppc64el.deb ... 408s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ... 408s Preparing to unpack .../031-libctf0_2.42-4ubuntu1_ppc64el.deb ... 408s Unpacking libctf0:ppc64el (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 408s Preparing to unpack .../032-libctf-nobfd0_2.42-4ubuntu1_ppc64el.deb ... 408s Unpacking libctf-nobfd0:ppc64el (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 409s Preparing to unpack .../033-binutils-powerpc64le-linux-gnu_2.42-4ubuntu1_ppc64el.deb ... 409s Unpacking binutils-powerpc64le-linux-gnu (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 409s Preparing to unpack .../034-libbinutils_2.42-4ubuntu1_ppc64el.deb ... 409s Unpacking libbinutils:ppc64el (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 409s Preparing to unpack .../035-binutils_2.42-4ubuntu1_ppc64el.deb ... 409s Unpacking binutils (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 409s Preparing to unpack .../036-binutils-common_2.42-4ubuntu1_ppc64el.deb ... 409s Unpacking binutils-common:ppc64el (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 409s Preparing to unpack .../037-libsframe1_2.42-4ubuntu1_ppc64el.deb ... 409s Unpacking libsframe1:ppc64el (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 409s Selecting previously unselected package libllvm18:ppc64el. 409s Preparing to unpack .../038-libllvm18_1%3a18.1.2-1ubuntu2_ppc64el.deb ... 409s Unpacking libllvm18:ppc64el (1:18.1.2-1ubuntu2) ... 410s Selecting previously unselected package libclang-cpp18. 410s Preparing to unpack .../039-libclang-cpp18_1%3a18.1.2-1ubuntu2_ppc64el.deb ... 410s Unpacking libclang-cpp18 (1:18.1.2-1ubuntu2) ... 410s Selecting previously unselected package libbpfcc:ppc64el. 410s Preparing to unpack .../040-libbpfcc_0.29.1+ds-1ubuntu4_ppc64el.deb ... 410s Unpacking libbpfcc:ppc64el (0.29.1+ds-1ubuntu4) ... 410s Selecting previously unselected package python3-bpfcc. 410s Preparing to unpack .../041-python3-bpfcc_0.29.1+ds-1ubuntu4_all.deb ... 410s Unpacking python3-bpfcc (0.29.1+ds-1ubuntu4) ... 410s Selecting previously unselected package ieee-data. 410s Preparing to unpack .../042-ieee-data_20220827.1_all.deb ... 410s Unpacking ieee-data (20220827.1) ... 410s Selecting previously unselected package python3-netaddr. 410s Preparing to unpack .../043-python3-netaddr_0.8.0-2ubuntu1_all.deb ... 410s Unpacking python3-netaddr (0.8.0-2ubuntu1) ... 410s Selecting previously unselected package bpfcc-tools. 410s Preparing to unpack .../044-bpfcc-tools_0.29.1+ds-1ubuntu4_all.deb ... 410s Unpacking bpfcc-tools (0.29.1+ds-1ubuntu4) ... 410s Selecting previously unselected package libclang1-18. 410s Preparing to unpack .../045-libclang1-18_1%3a18.1.2-1ubuntu2_ppc64el.deb ... 410s Unpacking libclang1-18 (1:18.1.2-1ubuntu2) ... 411s Selecting previously unselected package libdw1t64:ppc64el. 411s Preparing to unpack .../046-libdw1t64_0.190-1.1build2_ppc64el.deb ... 411s Unpacking libdw1t64:ppc64el (0.190-1.1build2) ... 411s Selecting previously unselected package bpftrace. 411s Preparing to unpack .../047-bpftrace_0.20.2-1ubuntu1_ppc64el.deb ... 411s Unpacking bpftrace (0.20.2-1ubuntu1) ... 411s Preparing to unpack .../048-cryptsetup-bin_2%3a2.7.0-1ubuntu2_ppc64el.deb ... 411s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 411s Preparing to unpack .../049-dpkg-dev_1.22.6ubuntu5_all.deb ... 411s Unpacking dpkg-dev (1.22.6ubuntu5) over (1.22.4ubuntu5) ... 411s Preparing to unpack .../050-libdpkg-perl_1.22.6ubuntu5_all.deb ... 411s Unpacking libdpkg-perl (1.22.6ubuntu5) over (1.22.4ubuntu5) ... 411s Selecting previously unselected package fonts-dejavu-mono. 411s Preparing to unpack .../051-fonts-dejavu-mono_2.37-8_all.deb ... 411s Unpacking fonts-dejavu-mono (2.37-8) ... 411s Selecting previously unselected package fonts-dejavu-core. 411s Preparing to unpack .../052-fonts-dejavu-core_2.37-8_all.deb ... 411s Unpacking fonts-dejavu-core (2.37-8) ... 411s Selecting previously unselected package fontconfig-config. 411s Preparing to unpack .../053-fontconfig-config_2.15.0-1.1ubuntu1_ppc64el.deb ... 411s Unpacking fontconfig-config (2.15.0-1.1ubuntu1) ... 411s Preparing to unpack .../054-libprotobuf-c1_1.4.1-1ubuntu3_ppc64el.deb ... 411s Unpacking libprotobuf-c1:ppc64el (1.4.1-1ubuntu3) over (1.4.1-1ubuntu2) ... 411s Preparing to unpack .../055-gnupg-l10n_2.4.4-2ubuntu15_all.deb ... 411s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 411s Preparing to unpack .../056-libibverbs1_50.0-2build1_ppc64el.deb ... 411s Unpacking libibverbs1:ppc64el (50.0-2build1) over (50.0-2) ... 411s Preparing to unpack .../057-ibverbs-providers_50.0-2build1_ppc64el.deb ... 411s Unpacking ibverbs-providers:ppc64el (50.0-2build1) over (50.0-2) ... 411s Preparing to unpack .../058-jq_1.7.1-3_ppc64el.deb ... 411s Unpacking jq (1.7.1-3) over (1.7.1-2) ... 411s Preparing to unpack .../059-libjq1_1.7.1-3_ppc64el.deb ... 411s Unpacking libjq1:ppc64el (1.7.1-3) over (1.7.1-2) ... 411s Selecting previously unselected package libaio1t64:ppc64el. 411s Preparing to unpack .../060-libaio1t64_0.3.113-6_ppc64el.deb ... 411s Unpacking libaio1t64:ppc64el (0.3.113-6) ... 411s Selecting previously unselected package libatm1t64:ppc64el. 411s Preparing to unpack .../061-libatm1t64_1%3a2.5.1-5.1_ppc64el.deb ... 411s Unpacking libatm1t64:ppc64el (1:2.5.1-5.1) ... 411s Selecting previously unselected package libc-dev-bin. 411s Preparing to unpack .../062-libc-dev-bin_2.39-0ubuntu6_ppc64el.deb ... 411s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 411s Selecting previously unselected package libfontconfig1:ppc64el. 411s Preparing to unpack .../063-libfontconfig1_2.15.0-1.1ubuntu1_ppc64el.deb ... 411s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu1) ... 411s Selecting previously unselected package libjpeg-turbo8:ppc64el. 411s Preparing to unpack .../064-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 411s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 411s Selecting previously unselected package libjpeg8:ppc64el. 411s Preparing to unpack .../065-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 411s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 411s Selecting previously unselected package libdeflate0:ppc64el. 411s Preparing to unpack .../066-libdeflate0_1.19-1_ppc64el.deb ... 411s Unpacking libdeflate0:ppc64el (1.19-1) ... 411s Selecting previously unselected package libjbig0:ppc64el. 411s Preparing to unpack .../067-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 411s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 411s Selecting previously unselected package liblerc4:ppc64el. 411s Preparing to unpack .../068-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 411s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 411s Selecting previously unselected package libsharpyuv0:ppc64el. 411s Preparing to unpack .../069-libsharpyuv0_1.3.2-0.4build2_ppc64el.deb ... 411s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4build2) ... 411s Selecting previously unselected package libwebp7:ppc64el. 411s Preparing to unpack .../070-libwebp7_1.3.2-0.4build2_ppc64el.deb ... 411s Unpacking libwebp7:ppc64el (1.3.2-0.4build2) ... 411s Selecting previously unselected package libtiff6:ppc64el. 411s Preparing to unpack .../071-libtiff6_4.5.1+git230720-4ubuntu1_ppc64el.deb ... 411s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu1) ... 411s Selecting previously unselected package libxpm4:ppc64el. 411s Preparing to unpack .../072-libxpm4_1%3a3.5.17-1build1_ppc64el.deb ... 411s Unpacking libxpm4:ppc64el (1:3.5.17-1build1) ... 412s Selecting previously unselected package libgd3:ppc64el. 412s Preparing to unpack .../073-libgd3_2.3.3-9ubuntu3_ppc64el.deb ... 412s Unpacking libgd3:ppc64el (2.3.3-9ubuntu3) ... 412s Selecting previously unselected package libc-devtools. 412s Preparing to unpack .../074-libc-devtools_2.39-0ubuntu6_ppc64el.deb ... 412s Unpacking libc-devtools (2.39-0ubuntu6) ... 412s Selecting previously unselected package linux-libc-dev:ppc64el. 412s Preparing to unpack .../075-linux-libc-dev_6.8.0-20.20_ppc64el.deb ... 412s Unpacking linux-libc-dev:ppc64el (6.8.0-20.20) ... 412s Selecting previously unselected package libcrypt-dev:ppc64el. 412s Preparing to unpack .../076-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 412s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 412s Selecting previously unselected package rpcsvc-proto. 412s Preparing to unpack .../077-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 412s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 412s Selecting previously unselected package libc6-dev:ppc64el. 412s Preparing to unpack .../078-libc6-dev_2.39-0ubuntu6_ppc64el.deb ... 412s Unpacking libc6-dev:ppc64el (2.39-0ubuntu6) ... 412s Preparing to unpack .../079-libevent-core-2.1-7_2.1.12-stable-9build1_ppc64el.deb ... 412s Unpacking libevent-core-2.1-7:ppc64el (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 412s Preparing to unpack .../080-libftdi1-2_1.5-6build4_ppc64el.deb ... 412s Unpacking libftdi1-2:ppc64el (1.5-6build4) over (1.5-6build3) ... 412s Preparing to unpack .../081-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ... 412s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 412s Selecting previously unselected package libunwind8:ppc64el. 412s Preparing to unpack .../082-libunwind8_1.6.2-3_ppc64el.deb ... 412s Unpacking libunwind8:ppc64el (1.6.2-3) ... 412s Selecting previously unselected package linux-modules-6.8.0-20-generic. 412s Preparing to unpack .../083-linux-modules-6.8.0-20-generic_6.8.0-20.20_ppc64el.deb ... 412s Unpacking linux-modules-6.8.0-20-generic (6.8.0-20.20) ... 412s Selecting previously unselected package linux-image-6.8.0-20-generic. 412s Preparing to unpack .../084-linux-image-6.8.0-20-generic_6.8.0-20.20_ppc64el.deb ... 412s Unpacking linux-image-6.8.0-20-generic (6.8.0-20.20) ... 413s Selecting previously unselected package linux-modules-extra-6.8.0-20-generic. 413s Preparing to unpack .../085-linux-modules-extra-6.8.0-20-generic_6.8.0-20.20_ppc64el.deb ... 413s Unpacking linux-modules-extra-6.8.0-20-generic (6.8.0-20.20) ... 414s Preparing to unpack .../086-linux-generic_6.8.0-20.20+1_ppc64el.deb ... 414s Unpacking linux-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 414s Preparing to unpack .../087-linux-image-generic_6.8.0-20.20+1_ppc64el.deb ... 414s Unpacking linux-image-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 414s Preparing to unpack .../088-linux-virtual_6.8.0-20.20+1_ppc64el.deb ... 414s Unpacking linux-virtual (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 414s Preparing to unpack .../089-linux-image-virtual_6.8.0-20.20+1_ppc64el.deb ... 414s Unpacking linux-image-virtual (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 414s Preparing to unpack .../090-linux-headers-virtual_6.8.0-20.20+1_ppc64el.deb ... 414s Unpacking linux-headers-virtual (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 414s Selecting previously unselected package linux-headers-6.8.0-20. 414s Preparing to unpack .../091-linux-headers-6.8.0-20_6.8.0-20.20_all.deb ... 414s Unpacking linux-headers-6.8.0-20 (6.8.0-20.20) ... 417s Selecting previously unselected package linux-headers-6.8.0-20-generic. 417s Preparing to unpack .../092-linux-headers-6.8.0-20-generic_6.8.0-20.20_ppc64el.deb ... 417s Unpacking linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 418s Preparing to unpack .../093-linux-headers-generic_6.8.0-20.20+1_ppc64el.deb ... 418s Unpacking linux-headers-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 418s Selecting previously unselected package linux-tools-common. 418s Preparing to unpack .../094-linux-tools-common_6.8.0-20.20_all.deb ... 418s Unpacking linux-tools-common (6.8.0-20.20) ... 418s Selecting previously unselected package linux-tools-6.8.0-20. 418s Preparing to unpack .../095-linux-tools-6.8.0-20_6.8.0-20.20_ppc64el.deb ... 418s Unpacking linux-tools-6.8.0-20 (6.8.0-20.20) ... 418s Selecting previously unselected package linux-tools-6.8.0-20-generic. 418s Preparing to unpack .../096-linux-tools-6.8.0-20-generic_6.8.0-20.20_ppc64el.deb ... 418s Unpacking linux-tools-6.8.0-20-generic (6.8.0-20.20) ... 418s Selecting previously unselected package manpages-dev. 418s Preparing to unpack .../097-manpages-dev_6.05.01-1_all.deb ... 418s Unpacking manpages-dev (6.05.01-1) ... 419s Preparing to unpack .../098-python3-distutils_3.12.2-3ubuntu1.1_all.deb ... 419s Unpacking python3-distutils (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 419s Preparing to unpack .../099-python3-lib2to3_3.12.2-3ubuntu1.1_all.deb ... 419s Unpacking python3-lib2to3 (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 419s Preparing to unpack .../100-python3-pyrsistent_0.20.0-1build1_ppc64el.deb ... 419s Unpacking python3-pyrsistent:ppc64el (0.20.0-1build1) over (0.20.0-1) ... 419s Preparing to unpack .../101-python3-typing-extensions_4.10.0-1_all.deb ... 419s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ... 419s Selecting previously unselected package ubuntu-kernel-accessories. 419s Preparing to unpack .../102-ubuntu-kernel-accessories_1.536build1_ppc64el.deb ... 419s Unpacking ubuntu-kernel-accessories (1.536build1) ... 419s Preparing to unpack .../103-kpartx_0.9.4-5ubuntu6_ppc64el.deb ... 419s Unpacking kpartx (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ... 419s Setting up pinentry-curses (1.2.1-3ubuntu4) ... 419s Setting up motd-news-config (13ubuntu8) ... 419s Setting up libtext-iconv-perl:ppc64el (1.7-8build2) ... 419s Setting up libtext-charwidth-perl:ppc64el (0.04-11build2) ... 419s Setting up libsharpyuv0:ppc64el (1.3.2-0.4build2) ... 419s Setting up liburcu8t64:ppc64el (0.14.0-3.1) ... 419s Setting up tcpdump (4.99.4-3ubuntu2) ... 419s Setting up libibverbs1:ppc64el (50.0-2build1) ... 419s Setting up systemd-sysv (255.4-1ubuntu5) ... 419s Setting up ubuntu-kernel-accessories (1.536build1) ... 419s Setting up libapparmor1:ppc64el (4.0.0-beta3-0ubuntu2) ... 419s Setting up libatm1t64:ppc64el (1:2.5.1-5.1) ... 419s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 419s Setting up libgdbm6t64:ppc64el (1.23-5.1) ... 419s Setting up bsdextrautils (2.39.3-9ubuntu2) ... 419s Setting up libxpm4:ppc64el (1:3.5.17-1build1) ... 419s Setting up libgdbm-compat4t64:ppc64el (1.23-5.1) ... 419s Setting up xdg-user-dirs (0.18-1) ... 419s Setting up ibverbs-providers:ppc64el (50.0-2build1) ... 419s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ... 419s Setting up libmagic-mgc (1:5.45-3) ... 419s Setting up gawk (1:5.2.1-2build2) ... 419s Setting up libjq1:ppc64el (1.7.1-3) ... 419s Setting up manpages (6.05.01-1) ... 419s Setting up libtirpc-common (1.3.4+ds-1.1) ... 419s Setting up libbrotli1:ppc64el (1.1.0-2build1) ... 419s Setting up libsqlite3-0:ppc64el (3.45.1-1ubuntu1) ... 419s Setting up libsasl2-modules:ppc64el (2.1.28+dfsg1-5ubuntu1) ... 419s Setting up libuv1t64:ppc64el (1.48.0-1.1) ... 419s Setting up libmagic1t64:ppc64el (1:5.45-3) ... 419s Setting up rsyslog (8.2312.0-3ubuntu7) ... 419s info: The user `syslog' is already a member of `adm'. 421s Setting up binutils-common:ppc64el (2.42-4ubuntu1) ... 421s Setting up libpsl5t64:ppc64el (0.21.2-1.1) ... 421s Setting up libnghttp2-14:ppc64el (1.59.0-1build1) ... 421s Setting up libdeflate0:ppc64el (1.19-1) ... 421s Setting up linux-libc-dev:ppc64el (6.8.0-20.20) ... 421s Setting up bc (1.07.1-3ubuntu2) ... 421s Setting up libctf-nobfd0:ppc64el (2.42-4ubuntu1) ... 421s Setting up libnss-systemd:ppc64el (255.4-1ubuntu5) ... 421s Setting up krb5-locales (1.20.1-6ubuntu1) ... 421s Setting up libcom-err2:ppc64el (1.47.0-2.4~exp1ubuntu2) ... 421s Setting up file (1:5.45-3) ... 421s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ... 421s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ... 421s Setting up libunwind8:ppc64el (1.6.2-3) ... 421s Setting up libprotobuf-c1:ppc64el (1.4.1-1ubuntu3) ... 421s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 421s Setting up xxd (2:9.1.0016-1ubuntu6) ... 421s Setting up libsframe1:ppc64el (2.42-4ubuntu1) ... 421s Setting up libelf1t64:ppc64el (0.190-1.1build2) ... 421s Setting up libkrb5support0:ppc64el (1.20.1-6ubuntu1) ... 421s Setting up libdw1t64:ppc64el (0.190-1.1build2) ... 421s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 421s Setting up eject (2.39.3-9ubuntu2) ... 421s Setting up apparmor (4.0.0-beta3-0ubuntu2) ... 421s Installing new version of config file /etc/apparmor.d/abstractions/authentication ... 421s Installing new version of config file /etc/apparmor.d/abstractions/crypto ... 421s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ... 421s Installing new version of config file /etc/apparmor.d/abstractions/openssl ... 421s Installing new version of config file /etc/apparmor.d/code ... 421s Installing new version of config file /etc/apparmor.d/firefox ... 422s Reloading AppArmor profiles 422s Setting up libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 422s No schema files found: doing nothing. 422s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 422s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 422s Setting up vim-common (2:9.1.0016-1ubuntu6) ... 422s Setting up gcc-13-base:ppc64el (13.2.0-21ubuntu1) ... 422s Setting up libqrtr-glib0:ppc64el (1.2.2-1ubuntu3) ... 422s Setting up libslang2:ppc64el (2.3.3-3build1) ... 422s Setting up libnvme1t64 (1.8-3) ... 422s Setting up mtr-tiny (0.95-1.1build1) ... 422s Setting up gnupg-l10n (2.4.4-2ubuntu15) ... 422s Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build6) ... 422s Setting up libdbus-1-3:ppc64el (1.14.10-4ubuntu2) ... 422s Setting up xz-utils (5.6.0-0.2) ... 422s Setting up perl-modules-5.38 (5.38.2-3.2) ... 422s Setting up libproc2-0:ppc64el (2:4.0.4-4ubuntu2) ... 422s Setting up fonts-dejavu-mono (2.37-8) ... 422s Setting up libpng16-16t64:ppc64el (1.6.43-3) ... 422s Setting up systemd-timesyncd (255.4-1ubuntu5) ... 423s Setting up libevent-core-2.1-7:ppc64el (2.1.12-stable-9build1) ... 423s Setting up libss2:ppc64el (1.47.0-2.4~exp1ubuntu2) ... 423s Setting up usb.ids (2024.03.18-1) ... 423s Setting up sudo (1.9.15p5-3ubuntu3) ... 423s Setting up fonts-dejavu-core (2.37-8) ... 423s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ... 423s Setting up gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) ... 423s Setting up libk5crypto3:ppc64el (1.20.1-6ubuntu1) ... 423s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 423s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ... 423s Setting up libwebp7:ppc64el (1.3.2-0.4build2) ... 423s Setting up libfdisk1:ppc64el (2.39.3-9ubuntu2) ... 423s Setting up libdb5.3t64:ppc64el (5.3.28+dfsg2-6) ... 423s Setting up libdevmapper1.02.1:ppc64el (2:1.02.185-3ubuntu2) ... 423s Setting up libaio1t64:ppc64el (0.3.113-6) ... 423s Setting up python-apt-common (2.7.7) ... 423s Setting up mount (2.39.3-9ubuntu2) ... 423s Setting up dmsetup (2:1.02.185-3ubuntu2) ... 423s Setting up uuid-runtime (2.39.3-9ubuntu2) ... 424s uuidd.service is a disabled or a static unit not running, not starting it. 424s Setting up libmm-glib0:ppc64el (1.23.4-0ubuntu1) ... 424s Setting up groff-base (1.23.0-3build1) ... 424s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 424s Setting up libplymouth5:ppc64el (24.004.60-1ubuntu6) ... 424s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ... 424s Setting up jq (1.7.1-3) ... 424s Setting up procps (2:4.0.4-4ubuntu2) ... 424s Setting up gpgconf (2.4.4-2ubuntu15) ... 424s Setting up libcryptsetup12:ppc64el (2:2.7.0-1ubuntu2) ... 424s Setting up libgirepository-1.0-1:ppc64el (1.79.1-1ubuntu6) ... 424s Setting up libjson-glib-1.0-common (1.8.0-2build1) ... 424s Setting up libkrb5-3:ppc64el (1.20.1-6ubuntu1) ... 424s Setting up libpython3.11-minimal:ppc64el (3.11.8-1build4) ... 424s Setting up libusb-1.0-0:ppc64el (2:1.0.27-1) ... 424s Setting up libperl5.38t64:ppc64el (5.38.2-3.2) ... 424s Setting up tnftp (20230507-2build1) ... 424s Setting up libbinutils:ppc64el (2.42-4ubuntu1) ... 424s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ... 424s Setting up libfido2-1:ppc64el (1.14.0-1build1) ... 424s Setting up libc-dev-bin (2.39-0ubuntu6) ... 424s Setting up openssl (3.0.13-0ubuntu2) ... 424s Setting up linux-modules-6.8.0-20-generic (6.8.0-20.20) ... 427s Setting up linux-tools-common (6.8.0-20.20) ... 427s Setting up readline-common (8.2-4) ... 427s Setting up libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu2) ... 427s Setting up libxmuu1:ppc64el (2:1.1.3-3build1) ... 427s Setting up dbus-bin (1.14.10-4ubuntu2) ... 427s Setting up info (7.1-3build1) ... 427s Setting up liblocale-gettext-perl (1.07-6ubuntu4) ... 427s Setting up gpg (2.4.4-2ubuntu15) ... 427s Setting up libgudev-1.0-0:ppc64el (1:238-3ubuntu2) ... 427s Setting up libpolkit-gobject-1-0:ppc64el (124-1ubuntu1) ... 427s Setting up libbpf1:ppc64el (1:1.3.0-2build1) ... 427s Setting up libmbim-glib4:ppc64el (1.31.2-0ubuntu2) ... 427s Setting up rsync (3.2.7-1build1) ... 428s rsync.service is a disabled or a static unit not running, not starting it. 428s Setting up libudisks2-0:ppc64el (2.10.1-6) ... 428s Setting up libkmod2:ppc64el (31+20240202-2ubuntu4) ... 428s Setting up bolt (0.9.6-2build1) ... 429s bolt.service is a disabled or a static unit not running, not starting it. 429s Setting up libllvm18:ppc64el (1:18.1.2-1ubuntu2) ... 429s Setting up gnupg-utils (2.4.4-2ubuntu15) ... 429s Setting up initramfs-tools-bin (0.142ubuntu23) ... 429s Setting up libctf0:ppc64el (2.42-4ubuntu1) ... 429s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 429s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ... 429s Setting up python3.11-minimal (3.11.8-1build4) ... 430s Setting up libclang1-18 (1:18.1.2-1ubuntu2) ... 430s Setting up manpages-dev (6.05.01-1) ... 430s Setting up linux-modules-extra-6.8.0-20-generic (6.8.0-20.20) ... 432s Setting up apt-utils (2.7.14) ... 432s Setting up gpg-agent (2.4.4-2ubuntu15) ... 432s Setting up libpython3.12-stdlib:ppc64el (3.12.2-4build3) ... 432s Setting up wget (1.21.4-1ubuntu2) ... 432s Setting up fontconfig-config (2.15.0-1.1ubuntu1) ... 432s Setting up libxmlb2:ppc64el (0.3.15-1build1) ... 432s Setting up libpython3.11-stdlib:ppc64el (3.11.8-1build4) ... 432s Setting up python3.12 (3.12.2-4build3) ... 434s Setting up gpgsm (2.4.4-2ubuntu15) ... 434s Setting up inetutils-telnet (2:2.5-3ubuntu3) ... 434s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ... 434s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ... 434s update-initramfs: deferring update (trigger activated) 434s e2scrub_all.service is a disabled or a static unit not running, not starting it. 434s Setting up linux-tools-6.8.0-20 (6.8.0-20.20) ... 434s Setting up libparted2t64:ppc64el (3.6-3.1build2) ... 434s Setting up linux-headers-generic (6.8.0-20.20+1) ... 434s Setting up dbus-daemon (1.14.10-4ubuntu2) ... 434s Setting up libmbim-proxy (1.31.2-0ubuntu2) ... 434s Setting up vim-tiny (2:9.1.0016-1ubuntu6) ... 434s Setting up kmod (31+20240202-2ubuntu4) ... 435s Setting up libnetplan1:ppc64el (1.0-1) ... 435s Setting up man-db (2.12.0-3build4) ... 435s Updating database of manual pages ... 437s man-db.service is a disabled or a static unit not running, not starting it. 437s Setting up fdisk (2.39.3-9ubuntu2) ... 437s Setting up libjson-glib-1.0-0:ppc64el (1.8.0-2build1) ... 437s Setting up libsasl2-modules-db:ppc64el (2.1.28+dfsg1-5ubuntu1) ... 437s Setting up libftdi1-2:ppc64el (1.5-6build4) ... 437s Setting up perl (5.38.2-3.2) ... 437s Setting up libfreetype6:ppc64el (2.13.2+dfsg-1build2) ... 437s Setting up linux-tools-6.8.0-20-generic (6.8.0-20.20) ... 437s Setting up gir1.2-girepository-2.0:ppc64el (1.79.1-1ubuntu6) ... 437s Setting up dbus (1.14.10-4ubuntu2) ... 437s A reboot is required to replace the running dbus-daemon. 437s Please reboot the system when convenient. 438s Setting up shared-mime-info (2.4-1build1) ... 438s Setting up libblockdev-utils3:ppc64el (3.1.0-1build1) ... 438s Setting up libgssapi-krb5-2:ppc64el (1.20.1-6ubuntu1) ... 438s Setting up udev (255.4-1ubuntu5) ... 439s Setting up ftp (20230507-2build1) ... 439s Setting up keyboxd (2.4.4-2ubuntu15) ... 439s Setting up libdpkg-perl (1.22.6ubuntu5) ... 439s Setting up libsasl2-2:ppc64el (2.1.28+dfsg1-5ubuntu1) ... 439s Setting up libssh-4:ppc64el (0.10.6-2build1) ... 439s Setting up libblockdev-nvme3:ppc64el (3.1.0-1build1) ... 439s Setting up libblockdev-fs3:ppc64el (3.1.0-1build1) ... 439s Setting up ieee-data (20220827.1) ... 439s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu1) ... 439s Setting up kpartx (0.9.4-5ubuntu6) ... 439s Setting up libpam-systemd:ppc64el (255.4-1ubuntu5) ... 439s Setting up libpolkit-agent-1-0:ppc64el (124-1ubuntu1) ... 439s Setting up libc6-dev:ppc64el (2.39-0ubuntu6) ... 439s Setting up libgpgme11t64:ppc64el (1.18.0-4.1ubuntu3) ... 439s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu1) ... 439s Setting up binutils-powerpc64le-linux-gnu (2.42-4ubuntu1) ... 439s Setting up netplan-generator (1.0-1) ... 439s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 439s Setting up initramfs-tools-core (0.142ubuntu23) ... 439s Setting up libclang-cpp18 (1:18.1.2-1ubuntu2) ... 439s Setting up libbpfcc:ppc64el (0.29.1+ds-1ubuntu4) ... 439s Setting up libarchive13t64:ppc64el (3.7.2-1.1ubuntu2) ... 439s Setting up libldap2:ppc64el (2.6.7+dfsg-1~exp1ubuntu6) ... 439s Setting up libpython3-stdlib:ppc64el (3.12.2-0ubuntu1) ... 439s Setting up systemd-resolved (255.4-1ubuntu5) ... 440s Setting up python3.11 (3.11.8-1build4) ... 441s Setting up telnet (0.17+2.5-3ubuntu3) ... 441s Setting up initramfs-tools (0.142ubuntu23) ... 441s update-initramfs: deferring update (trigger activated) 441s Setting up libblockdev-mdraid3:ppc64el (3.1.0-1build1) ... 441s Setting up linux-headers-virtual (6.8.0-20.20+1) ... 441s Setting up libcurl4t64:ppc64el (8.5.0-2ubuntu8) ... 441s Setting up bpftrace (0.20.2-1ubuntu1) ... 441s Setting up bind9-libs:ppc64el (1:9.18.24-0ubuntu3) ... 441s Setting up linux-image-6.8.0-20-generic (6.8.0-20.20) ... 444s I: /boot/vmlinux is now a symlink to vmlinux-6.8.0-20-generic 444s I: /boot/initrd.img is now a symlink to initrd.img-6.8.0-20-generic 444s Setting up libtirpc3t64:ppc64el (1.3.4+ds-1.1) ... 444s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ... 444s Setting up libblockdev-swap3:ppc64el (3.1.0-1build1) ... 444s Setting up plymouth (24.004.60-1ubuntu6) ... 444s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 444s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 450s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 450s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 451s Setting up iproute2 (6.1.0-1ubuntu5) ... 451s Setting up openssh-client (1:9.6p1-3ubuntu11) ... 451s Setting up libgusb2:ppc64el (0.4.8-1build1) ... 451s Setting up btrfs-progs (6.6.3-1.1build1) ... 451s Setting up libblockdev-loop3:ppc64el (3.1.0-1build1) ... 451s Setting up libcurl3t64-gnutls:ppc64el (8.5.0-2ubuntu8) ... 451s Setting up parted (3.6-3.1build2) ... 451s Setting up libqmi-glib5:ppc64el (1.35.2-0ubuntu1) ... 451s Setting up python3 (3.12.2-0ubuntu1) ... 451s Setting up binutils (2.42-4ubuntu1) ... 451s Setting up libblockdev3:ppc64el (3.1.0-1build1) ... 451s Setting up libjcat1:ppc64el (0.2.0-2build2) ... 451s Setting up multipath-tools (0.9.4-5ubuntu6) ... 452s Setting up dpkg-dev (1.22.6ubuntu5) ... 452s Setting up libblockdev-part3:ppc64el (3.1.0-1build1) ... 452s Setting up dirmngr (2.4.4-2ubuntu15) ... 452s Setting up dbus-user-session (1.14.10-4ubuntu2) ... 452s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ... 452s update-initramfs: deferring update (trigger activated) 452s Setting up python3-cryptography (41.0.7-4build2) ... 452s Setting up python3-gi (3.47.0-3build1) ... 453s Setting up libgd3:ppc64el (2.3.3-9ubuntu3) ... 453s Setting up python3-typing-extensions (4.10.0-1) ... 453s Setting up lsof (4.95.0-1build2) ... 453s Setting up python3-pyrsistent:ppc64el (0.20.0-1build1) ... 453s Setting up python3-netaddr (0.8.0-2ubuntu1) ... 453s Setting up libnsl2:ppc64el (1.3.0-3build2) ... 453s Setting up gnupg (2.4.4-2ubuntu15) ... 453s Setting up python3-netplan (1.0-1) ... 453s Setting up curl (8.5.0-2ubuntu8) ... 453s Setting up libvolume-key1:ppc64el (0.3.12-7build1) ... 453s Setting up linux-image-virtual (6.8.0-20.20+1) ... 453s Setting up bind9-host (1:9.18.24-0ubuntu3) ... 453s Setting up python3-lib2to3 (3.12.2-3ubuntu1.1) ... 453s Setting up python3-bpfcc (0.29.1+ds-1ubuntu4) ... 454s Setting up libc-devtools (2.39-0ubuntu6) ... 454s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... 454s Setting up python3-distutils (3.12.2-3ubuntu1.1) ... 454s python3.12: can't get files for byte-compilation 454s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ... 454s Setting up linux-image-generic (6.8.0-20.20+1) ... 454s Setting up python3-dbus (1.3.2-5build2) ... 454s Setting up python3-setuptools (68.1.2-2ubuntu1) ... 455s Setting up gpg-wks-client (2.4.4-2ubuntu15) ... 455s Setting up openssh-server (1:9.6p1-3ubuntu11) ... 455s Replacing config file /etc/ssh/sshd_config with new version 457s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket. 458s Setting up linux-generic (6.8.0-20.20+1) ... 458s Setting up libblockdev-crypto3:ppc64el (3.1.0-1build1) ... 458s Setting up python3-gdbm:ppc64el (3.12.2-3ubuntu1.1) ... 458s Setting up python3-apt (2.7.7) ... 458s Setting up libfwupd2:ppc64el (1.9.15-2) ... 458s Setting up python3-yaml (6.0.1-2build1) ... 459s Setting up libqmi-proxy (1.35.2-0ubuntu1) ... 459s Setting up netplan.io (1.0-1) ... 459s Setting up linux-virtual (6.8.0-20.20+1) ... 459s Setting up grub-common (2.12-1ubuntu5) ... 459s Setting up bpfcc-tools (0.29.1+ds-1ubuntu4) ... 459s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ... 459s Setting up ubuntu-pro-client (31.2.2) ... 461s Setting up fwupd (1.9.15-2) ... 462s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 462s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 462s Setting up ubuntu-pro-client-l10n (31.2.2) ... 462s Setting up udisks2 (2.10.1-6) ... 462s Setting up grub2-common (2.12-1ubuntu5) ... 462s Setting up grub-ieee1275-bin (2.12-1ubuntu5) ... 462s Setting up grub-ieee1275 (2.12-1ubuntu5) ... 463s Installing for powerpc-ieee1275 platform. 463s Installation finished. No error reported. 463s Sourcing file `/etc/default/grub' 463s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 463s Generating grub configuration file ... 463s Found linux image: /boot/vmlinux-6.8.0-20-generic 463s Found linux image: /boot/vmlinux-6.8.0-11-generic 463s Found initrd image: /boot/initrd.img-6.8.0-11-generic 463s Warning: os-prober will not be executed to detect other bootable partitions. 463s Systems on them will not be added to the GRUB boot configuration. 463s Check GRUB_DISABLE_OS_PROBER documentation entry. 463s Adding boot menu entry for UEFI Firmware Settings ... 463s done 463s Processing triggers for ufw (0.36.2-5) ... 463s Processing triggers for systemd (255.4-1ubuntu5) ... 463s Processing triggers for debianutils (5.17) ... 463s Processing triggers for install-info (7.1-3build1) ... 464s Processing triggers for libc-bin (2.39-0ubuntu6) ... 464s Processing triggers for initramfs-tools (0.142ubuntu23) ... 464s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 464s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 469s Processing triggers for linux-image-6.8.0-20-generic (6.8.0-20.20) ... 469s /etc/kernel/postinst.d/initramfs-tools: 469s update-initramfs: Generating /boot/initrd.img-6.8.0-20-generic 469s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 476s /etc/kernel/postinst.d/zz-update-grub: 476s Sourcing file `/etc/default/grub' 476s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 476s Generating grub configuration file ... 476s Found linux image: /boot/vmlinux-6.8.0-20-generic 476s Found initrd image: /boot/initrd.img-6.8.0-20-generic 476s Found linux image: /boot/vmlinux-6.8.0-11-generic 476s Found initrd image: /boot/initrd.img-6.8.0-11-generic 476s Warning: os-prober will not be executed to detect other bootable partitions. 476s Systems on them will not be added to the GRUB boot configuration. 476s Check GRUB_DISABLE_OS_PROBER documentation entry. 476s Adding boot menu entry for UEFI Firmware Settings ... 476s done 477s Reading package lists... 477s Building dependency tree... 477s Reading state information... 478s The following packages will be REMOVED: 478s libaio1* libnetplan0* python3-distutils* python3-lib2to3* 478s 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded. 478s After this operation, 1613 kB disk space will be freed. 478s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 112169 files and directories currently installed.) 478s Removing libaio1:ppc64el (0.3.113-5) ... 478s Removing libnetplan0:ppc64el (0.107.1-3) ... 478s Removing python3-distutils (3.12.2-3ubuntu1.1) ... 478s Removing python3-lib2to3 (3.12.2-3ubuntu1.1) ... 478s Processing triggers for libc-bin (2.39-0ubuntu6) ... 478s autopkgtest [08:28:52]: rebooting testbed after setup commands that affected boot 598s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 621s autopkgtest [08:31:15]: testbed running kernel: Linux 6.8.0-20-generic #20-Ubuntu SMP Mon Mar 18 11:46:05 UTC 2024 625s autopkgtest [08:31:19]: @@@@@@@@@@@@@@@@@@@@ apt-source bowtie2 628s Get:1 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (dsc) [2513 B] 628s Get:2 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (tar) [10.6 MB] 628s Get:3 http://ftpmaster.internal/ubuntu noble/universe bowtie2 2.5.2-1 (diff) [19.8 kB] 629s gpgv: Signature made Wed Jan 10 20:06:52 2024 UTC 629s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 629s gpgv: issuer "tillea@rki.de" 629s gpgv: Can't check signature: No public key 629s dpkg-source: warning: cannot verify inline signature for ./bowtie2_2.5.2-1.dsc: no acceptable signature found 629s autopkgtest [08:31:23]: testing package bowtie2 version 2.5.2-1 630s autopkgtest [08:31:24]: build not needed 647s autopkgtest [08:31:41]: test run-unit-test: preparing testbed 649s Reading package lists... 649s Building dependency tree... 649s Reading state information... 649s Starting pkgProblemResolver with broken count: 0 649s Starting 2 pkgProblemResolver with broken count: 0 649s Done 649s The following additional packages will be installed: 649s bowtie2 bowtie2-examples libclone-perl libconfig-general-perl 649s libfile-which-perl libmath-random-perl libsys-info-base-perl 649s libsys-info-driver-linux-perl libsys-info-perl libtest-deep-perl 649s libunix-processors-perl 649s The following NEW packages will be installed: 649s autopkgtest-satdep bowtie2 bowtie2-examples libclone-perl 649s libconfig-general-perl libfile-which-perl libmath-random-perl 649s libsys-info-base-perl libsys-info-driver-linux-perl libsys-info-perl 649s libtest-deep-perl libunix-processors-perl 649s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 649s Need to get 11.3 MB/11.3 MB of archives. 649s After this operation, 15.1 MB of additional disk space will be used. 649s Get:1 /tmp/autopkgtest.XTISEH/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [760 B] 649s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libclone-perl ppc64el 0.46-1build2 [11.1 kB] 650s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libconfig-general-perl all 2.65-2 [57.1 kB] 650s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-which-perl all 1.27-2 [12.5 kB] 650s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el libmath-random-perl ppc64el 0.72-2build4 [52.3 kB] 650s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsys-info-base-perl all 0.7807-4 [27.0 kB] 650s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libunix-processors-perl ppc64el 2.046-3build3 [15.8 kB] 650s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsys-info-driver-linux-perl all 0.7905-6 [24.1 kB] 650s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsys-info-perl all 0.7811-3 [6662 B] 650s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtest-deep-perl all 1.204-1 [47.1 kB] 650s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie2 ppc64el 2.5.2-1 [1367 kB] 650s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie2-examples all 2.5.2-1 [9707 kB] 651s Fetched 11.3 MB in 1s (8007 kB/s) 651s Selecting previously unselected package libclone-perl:ppc64el. 651s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 111945 files and directories currently installed.) 651s Preparing to unpack .../00-libclone-perl_0.46-1build2_ppc64el.deb ... 651s Unpacking libclone-perl:ppc64el (0.46-1build2) ... 651s Selecting previously unselected package libconfig-general-perl. 651s Preparing to unpack .../01-libconfig-general-perl_2.65-2_all.deb ... 651s Unpacking libconfig-general-perl (2.65-2) ... 651s Selecting previously unselected package libfile-which-perl. 651s Preparing to unpack .../02-libfile-which-perl_1.27-2_all.deb ... 651s Unpacking libfile-which-perl (1.27-2) ... 651s Selecting previously unselected package libmath-random-perl. 651s Preparing to unpack .../03-libmath-random-perl_0.72-2build4_ppc64el.deb ... 651s Unpacking libmath-random-perl (0.72-2build4) ... 651s Selecting previously unselected package libsys-info-base-perl. 651s Preparing to unpack .../04-libsys-info-base-perl_0.7807-4_all.deb ... 651s Unpacking libsys-info-base-perl (0.7807-4) ... 651s Selecting previously unselected package libunix-processors-perl:ppc64el. 651s Preparing to unpack .../05-libunix-processors-perl_2.046-3build3_ppc64el.deb ... 651s Unpacking libunix-processors-perl:ppc64el (2.046-3build3) ... 651s Selecting previously unselected package libsys-info-driver-linux-perl. 651s Preparing to unpack .../06-libsys-info-driver-linux-perl_0.7905-6_all.deb ... 651s Unpacking libsys-info-driver-linux-perl (0.7905-6) ... 651s Selecting previously unselected package libsys-info-perl. 651s Preparing to unpack .../07-libsys-info-perl_0.7811-3_all.deb ... 651s Unpacking libsys-info-perl (0.7811-3) ... 651s Selecting previously unselected package libtest-deep-perl. 651s Preparing to unpack .../08-libtest-deep-perl_1.204-1_all.deb ... 651s Unpacking libtest-deep-perl (1.204-1) ... 651s Selecting previously unselected package bowtie2. 651s Preparing to unpack .../09-bowtie2_2.5.2-1_ppc64el.deb ... 651s Unpacking bowtie2 (2.5.2-1) ... 651s Selecting previously unselected package bowtie2-examples. 651s Preparing to unpack .../10-bowtie2-examples_2.5.2-1_all.deb ... 651s Unpacking bowtie2-examples (2.5.2-1) ... 651s Selecting previously unselected package autopkgtest-satdep. 651s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 651s Unpacking autopkgtest-satdep (0) ... 651s Setting up libfile-which-perl (1.27-2) ... 651s Setting up libconfig-general-perl (2.65-2) ... 651s Setting up libtest-deep-perl (1.204-1) ... 651s Setting up libmath-random-perl (0.72-2build4) ... 651s Setting up libclone-perl:ppc64el (0.46-1build2) ... 651s Setting up bowtie2 (2.5.2-1) ... 651s Setting up libunix-processors-perl:ppc64el (2.046-3build3) ... 651s Setting up bowtie2-examples (2.5.2-1) ... 651s Setting up libsys-info-base-perl (0.7807-4) ... 651s Setting up libsys-info-driver-linux-perl (0.7905-6) ... 651s Setting up libsys-info-perl (0.7811-3) ... 652s Setting up autopkgtest-satdep (0) ... 652s Processing triggers for man-db (2.12.0-3build4) ... 655s (Reading database ... 112205 files and directories currently installed.) 655s Removing autopkgtest-satdep (0) ... 655s autopkgtest [08:31:49]: test run-unit-test: [----------------------- 656s \1 better written as $1 at simple_tests.pl line 4674. 656s \1 better written as $1 at simple_tests.pl line 4675. 656s FASTA-continuous 1 (fw:1, sam:1) 656s References: 656s >0 656s AGCATCGATCAGTATCTGA 656s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 656s /usr/bin/bowtie2 -F 10,9 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:19 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz" 656s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s FASTA-continuous 2 (fw:1, sam:1) 656s References: 656s >0 656s AGCATCGATCAGTATCTGA 656s /usr/bin/bowtie2 -F 10,9 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:19 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz" 656s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s seq2_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s FASTA-continuous 3 (fw:1, sam:1) 656s References: 656s >0 656s AGCATCGATCAGTATCTGA 656s /usr/bin/bowtie2 -F 10,9 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:19 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz" 656s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s FASTA-continuous 4 (fw:1, sam:1) 656s References: 656s >0 656s AGCATCGATCAGTATCTGA 656s /usr/bin/bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:19 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz" 656s seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s FASTA-continuous 5 (fw:1, sam:1) 656s References: 656s >0 656s AGCATCGATCAGTATCTGA 656s /usr/bin/bowtie2 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:19 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz" 656s seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s FASTA-continuous 6 (fw:1, sam:1) 656s References: 656s >0 656s AGCATCGATCAG 656s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 656s /usr/bin/bowtie2 -F 10,1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz 656s @HD VN:1.5 SO:unsorted GO:query 656s @SQ SN:0 LN:12 656s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz" 656s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s seq1_1 0 0 2 255 10M * 0 0 GCATCGATCA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s seq1_2 0 0 3 255 10M * 0 0 CATCGATCAG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 656s Align should not fail when first seq in ref is all Ns (fw:1, sam:1) 656s References: 656s >0 656s NNNNNNNNNNNNNNN 656s >1 656s AGCATCGATCAGTATCTGA 656s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 656s Warning: Encountered reference sequence with only gaps 657s Warning: Encountered reference sequence with only gaps 657s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:15 657s @SQ SN:1 LN:19 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 657s 0 0 1 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 657s Align should not fail when multiple seqs are all Ns (fw:1, sam:1) 657s References: 657s >0 657s NNNNNNNNNNNNNNN 657s >1 657s NNNNNNNNNNNNNNN 657s >2 657s AGCATCGATCAGTATCTGA 657s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 657s Warning: Encountered reference sequence with only gaps 657s Warning: Encountered reference sequence with only gaps 657s Warning: Encountered reference sequence with only gaps 657s Warning: Encountered reference sequence with only gaps 657s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:15 657s @SQ SN:1 LN:15 657s @SQ SN:2 LN:19 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 657s 0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 657s Should account for stretch of Ns at beginning (fw:1, sam:1) 657s References: 657s >0 657s NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA 657s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 657s /usr/bin/bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:34 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 657s 0 0 0 18 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 657s Cline 1 (fw:1, sam:1) 657s References: 657s >0 657s AGCATCGATCAGTATCTGA 657s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 657s /usr/bin/bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:19 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 657s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 657s Cline 2 (fw:1, sam:1) 657s References: 657s >0 657s AGCATCGATCAGTATCTGA 657s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:19 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 657s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 657s Cline 2 (fw:1, sam:1) 657s References: 657s >0 657s AGCATCGATCAGTATCTGA 657s /usr/bin/bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP 657s @HD VN:1.5 SO:unsorted GO:query 657s @SQ SN:0 LN:19 657s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" 657s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG ABCDEDGHIJKLMNOP AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 657s Cline 4 (fw:1, sam:1) 657s References: 657s >0 657s AGCATCGATCAGTATCTGA 657s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO 657s Error: Read 0 has more read characters than quality values. 657s terminate called after throwing an instance of 'int' 658s Aborted (core dumped) 658s (ERR): bowtie2-align exited with value 134 658s Cline 5 (fw:1, sam:1) 658s References: 658s >0 658s AGCATCGATCAGTATCTGA 658s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ 658s Error: Read 0 has more quality values than read characters. 658s terminate called after throwing an instance of 'int' 658s Aborted (core dumped) 658s (ERR): bowtie2-align exited with value 134 658s trim-to: trim from 5'-end (fw:1, sam:1) 658s References: 658s >0 658s AGCATCGATCAGTATCTGA 658s /usr/bin/bowtie2 --trim-to 5:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 658s 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:19 658s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 658s 0 0 0 7 255 12M * 0 0 GATCAGTATCTG IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 658s trim-to: trim from 3'-end (fw:1, sam:1) 658s References: 658s >0 658s AGCATCGATCAGTATCTGA 658s /usr/bin/bowtie2 --trim-to 3:12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 658s 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:19 658s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 658s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 658s trim-to: trim from 3'-end (default) (fw:1, sam:1) 658s References: 658s >0 658s AGCATCGATCAGTATCTGA 658s /usr/bin/bowtie2 --trim-to 12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 658s 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:19 658s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 658s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 658s trim-to: invalid position (fw:1, sam:1) 658s References: 658s >0 658s AGCATCGATCAGTATCTGA 658s /usr/bin/bowtie2 --trim-to 4:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 658s 658s --trim-to: trim position must be either 3 or 5 658s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 658s Usage: 658s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 658s 658s Index filename prefix (minus trailing .X.bt2). 658s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 658s Files with #1 mates, paired with files in . 658s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 658s Files with #2 mates, paired with files in . 658s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 658s Files with unpaired reads. 658s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 658s Files with interleaved paired-end FASTQ/FASTA reads 658s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 658s Files are unaligned BAM sorted by read name. 658s File for SAM output (default: stdout) 658s 658s , , can be comma-separated lists (no whitespace) and can be 658s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 658s 658s Options (defaults in parentheses): 658s 658s Input: 658s trim-to: invalid count (fw:1, sam:1) 658s References: 658s >0 658s AGCATCGATCAGTATCTGA 658s /usr/bin/bowtie2 --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 658s 658s -q query input files are FASTQ .fq/.fastq (default) 658s --tab5 query input files are TAB5 .tab5 658s --tab6 query input files are TAB6 .tab6 658s --qseq query input files are in Illumina's qseq format 658s -f query input files are (multi-)FASTA .fa/.mfa 658s -r query input files are raw one-sequence-per-line 658s -F k:,i: query input files are continuous FASTA where reads 658s are substrings (k-mers) extracted from a FASTA file 658s and aligned at offsets 1, 1+i, 1+2i ... end of reference 658s -c , , are sequences themselves, not files 658s -s/--skip skip the first reads/pairs in the input (none) 658s -u/--upto stop after first reads/pairs (no limit) 658s -5/--trim5 trim bases from 5'/left end of reads (0) 658s -3/--trim3 trim bases from 3'/right end of reads (0) 658s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 658s If the read end is not specified then it defaults to 3 (0) 658s --phred33 qualities are Phred+33 (default) 658s --phred64 qualities are Phred+64 658s --int-quals qualities encoded as space-delimited integers 658s 658s Presets: Same as: 658s For --end-to-end: 658s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 658s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 658s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 658s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 658s 658s For --local: 658s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 658s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 658s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 658s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 658s 658s Alignment: 658s -N max # mismatches in seed alignment; can be 0 or 1 (0) 658s -L length of seed substrings; must be >3, <32 (22) 658s -i interval between seed substrings w/r/t read len (S,1,1.15) 658s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 658s --dpad include extra ref chars on sides of DP table (15) 658s --gbar disallow gaps within nucs of read extremes (4) 658s --ignore-quals treat all quality values as 30 on Phred scale (off) 658s --nofw do not align forward (original) version of read (off) 658s --norc do not align reverse-complement version of read (off) 658s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 658s scan for the optimal seeded alignments 658s --end-to-end entire read must align; no clipping (on) 658s OR 658s --local local alignment; ends might be soft clipped (off) 658s 658s Scoring: 658s --ma match bonus (0 for --end-to-end, 2 for --local) 658s --mp max penalty for mismatch; lower qual = lower penalty (6) 658s --np penalty for non-A/C/G/Ts in read/ref (1) 658s --rdg , read gap open, extend penalties (5,3) 658s --rfg , reference gap open, extend penalties (5,3) 658s --score-min min acceptable alignment score w/r/t read length 658s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 658s 658s Reporting: 658s (default) look for multiple alignments, report best, with MAPQ 658s OR 658s -k report up to alns per read; MAPQ not meaningful 658s OR 658s -a/--all report all alignments; very slow, MAPQ not meaningful 658s 658s Effort: 658s -D give up extending after failed extends in a row (15) 658s -R for reads w/ repetitive seeds, try sets of seeds (2) 658s 658s Paired-end: 658s -I/--minins minimum fragment length (0) 658s -X/--maxins maximum fragment length (500) 658s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 658s --no-mixed suppress unpaired alignments for paired reads 658s --no-discordant suppress discordant alignments for paired reads 658s --dovetail concordant when mates extend past each other 658s --no-contain not concordant when one mate alignment contains other 658s --no-overlap not concordant when mates overlap at all 658s 658s BAM: 658s --align-paired-reads 658s Bowtie2 will, by default, attempt to align unpaired BAM reads. 658s Use this option to align paired-end reads instead. 658s --preserve-tags Preserve tags from the original BAM record by 658s appending them to the end of the corresponding SAM output. 658s 658s Output: 658s -t/--time print wall-clock time taken by search phases 658s --un write unpaired reads that didn't align to 658s --al write unpaired reads that aligned at least once to 658s --un-conc write pairs that didn't align concordantly to 658s --al-conc write pairs that aligned concordantly at least once to 658s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 658s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 658s --quiet print nothing to stderr except serious errors 658s --met-file send metrics to file at (off) 658s --met-stderr send metrics to stderr (off) 658s --met report internal counters & metrics every secs (1) 658s --no-unal suppress SAM records for unaligned reads 658s --no-head suppress header lines, i.e. lines starting with @ 658s --no-sq suppress @SQ header lines 658s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 658s --rg add ("lab:value") to @RG line of SAM header. 658s Note: @RG line only printed when --rg-id is set. 658s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 658s --sam-no-qname-trunc 658s Suppress standard behavior of truncating readname at first whitespace 658s at the expense of generating non-standard SAM. 658s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 658s --soft-clipped-unmapped-tlen 658s Exclude soft-clipped bases when reporting TLEN 658s --sam-append-comment 658s Append FASTA/FASTQ comment to SAM record 658s 658s Performance: 658s -p/--threads number of alignment threads to launch (1) 658s --reorder force SAM output order to match order of input reads 658s --mm use memory-mapped I/O for index; many 'bowtie's can share 658s 658s Other: 658s --qc-filter filter out reads that are bad according to QSEQ filter 658s --seed seed for random number generator (0) 658s --non-deterministic 658s seed rand. gen. arbitrarily instead of using read attributes 658s --version print version information and quit 658s -h/--help print this usage message 658s Error: Encountered internal Bowtie 2 exception (#1) 658s Command: /usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 658s (ERR): bowtie2-align exited with value 1 658s --trim-to: the number bases to trim must be at least 0 658s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 658s Usage: 658s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 658s 658s Index filename prefix (minus trailing .X.bt2). 658s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 658s Files with #1 mates, paired with files in . 658s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 658s Files with #2 mates, paired with files in . 658s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 658s Files with unpaired reads. 658s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 658s Files with interleaved paired-end FASTQ/FASTA reads 658s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 658s Files are unaligned BAM sorted by read name. 658s File for SAM output (default: stdout) 658s 658s , , can be comma-separated lists (no whitespace) and can be 658s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 658s 658s Cline 7 (fw:1, sam:1) 658s References: 658s >0 658s AGCATCGATCAGTATCTGA 658s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 658s 658s Options (defaults in parentheses): 658s 658s Input: 658s -q query input files are FASTQ .fq/.fastq (default) 658s --tab5 query input files are TAB5 .tab5 658s --tab6 query input files are TAB6 .tab6 658s --qseq query input files are in Illumina's qseq format 658s -f query input files are (multi-)FASTA .fa/.mfa 658s -r query input files are raw one-sequence-per-line 658s -F k:,i: query input files are continuous FASTA where reads 658s are substrings (k-mers) extracted from a FASTA file 658s and aligned at offsets 1, 1+i, 1+2i ... end of reference 658s -c , , are sequences themselves, not files 658s -s/--skip skip the first reads/pairs in the input (none) 658s -u/--upto stop after first reads/pairs (no limit) 658s -5/--trim5 trim bases from 5'/left end of reads (0) 658s -3/--trim3 trim bases from 3'/right end of reads (0) 658s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 658s If the read end is not specified then it defaults to 3 (0) 658s --phred33 qualities are Phred+33 (default) 658s --phred64 qualities are Phred+64 658s --int-quals qualities encoded as space-delimited integers 658s 658s Presets: Same as: 658s For --end-to-end: 658s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 658s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 658s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 658s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 658s 658s For --local: 658s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 658s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 658s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 658s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 658s 658s Alignment: 658s -N max # mismatches in seed alignment; can be 0 or 1 (0) 658s -L length of seed substrings; must be >3, <32 (22) 658s -i interval between seed substrings w/r/t read len (S,1,1.15) 658s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 658s --dpad include extra ref chars on sides of DP table (15) 658s --gbar disallow gaps within nucs of read extremes (4) 658s --ignore-quals treat all quality values as 30 on Phred scale (off) 658s --nofw do not align forward (original) version of read (off) 658s --norc do not align reverse-complement version of read (off) 658s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 658s scan for the optimal seeded alignments 658s --end-to-end entire read must align; no clipping (on) 658s OR 658s --local local alignment; ends might be soft clipped (off) 658s 658s Scoring: 658s --ma match bonus (0 for --end-to-end, 2 for --local) 658s --mp max penalty for mismatch; lower qual = lower penalty (6) 658s --np penalty for non-A/C/G/Ts in read/ref (1) 658s --rdg , read gap open, extend penalties (5,3) 658s --rfg , reference gap open, extend penalties (5,3) 658s --score-min min acceptable alignment score w/r/t read length 658s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 658s 658s Reporting: 658s (default) look for multiple alignments, report best, with MAPQ 658s OR 658s -k report up to alns per read; MAPQ not meaningful 658s OR 658s -a/--all report all alignments; very slow, MAPQ not meaningful 658s 658s Effort: 658s -D give up extending after failed extends in a row (15) 658s -R for reads w/ repetitive seeds, try sets of seeds (2) 658s 658s Paired-end: 658s -I/--minins minimum fragment length (0) 658s -X/--maxins maximum fragment length (500) 658s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 658s --no-mixed suppress unpaired alignments for paired reads 658s --no-discordant suppress discordant alignments for paired reads 658s --dovetail concordant when mates extend past each other 658s --no-contain not concordant when one mate alignment contains other 658s --no-overlap not concordant when mates overlap at all 658s 658s BAM: 658s --align-paired-reads 658s Bowtie2 will, by default, attempt to align unpaired BAM reads. 658s Use this option to align paired-end reads instead. 658s --preserve-tags Preserve tags from the original BAM record by 658s appending them to the end of the corresponding SAM output. 658s 658s Output: 658s -t/--time print wall-clock time taken by search phases 658s --un write unpaired reads that didn't align to 658s --al write unpaired reads that aligned at least once to 658s --un-conc write pairs that didn't align concordantly to 658s --al-conc write pairs that aligned concordantly at least once to 658s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 658s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 658s --quiet print nothing to stderr except serious errors 658s --met-file send metrics to file at (off) 658s --met-stderr send metrics to stderr (off) 658s --met report internal counters & metrics every secs (1) 658s --no-unal suppress SAM records for unaligned reads 658s --no-head suppress header lines, i.e. lines starting with @ 658s --no-sq suppress @SQ header lines 658s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 658s --rg add ("lab:value") to @RG line of SAM header. 658s Note: @RG line only printed when --rg-id is set. 658s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 658s --sam-no-qname-trunc 658s Suppress standard behavior of truncating readname at first whitespace 658s at the expense of generating non-standard SAM. 658s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 658s --soft-clipped-unmapped-tlen 658s Exclude soft-clipped bases when reporting TLEN 658s --sam-append-comment 658s Append FASTA/FASTQ comment to SAM record 658s 658s Performance: 658s -p/--threads number of alignment threads to launch (1) 658s --reorder force SAM output order to match order of input reads 658s --mm use memory-mapped I/O for index; many 'bowtie's can share 658s 658s Other: 658s --qc-filter filter out reads that are bad according to QSEQ filter 658s --seed seed for random number generator (0) 658s --non-deterministic 658s seed rand. gen. arbitrarily instead of using read attributes 658s --version print version information and quit 658s -h/--help print this usage message 658s Error: Encountered internal Bowtie 2 exception (#1) 658s Command: /usr/bin/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 658s (ERR): bowtie2-align exited with value 1 658s @HD VN:1.5 SO:unsorted GO:query 658s @SQ SN:0 LN:19 658s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 658s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 659s Cline 8 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 659s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 659s Cline 9 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 659s Cline multiread 1 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 659s 659s 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 659s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 659s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 659s Cline multiread 2 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 659s 659s 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 659s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 659s Cline multiread 3 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG 659s 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 659s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 659s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 659s Cline paired 1 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAAAAACTGA 659s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 659s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" 659s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 659s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 659s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 659s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 659s Cline paired 2 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAAAAACTGA 659s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 659s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 659s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 659s Cline paired 3 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAAAAACTGA 659s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 659s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 659s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 659s Cline paired 4 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAAAAACTGA 659s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 659s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 659s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 659s Fastq 1 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 659s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz" 659s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 659s Fastq 2 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" 659s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 659s Fastq 3 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz 659s @HD VN:1.5 SO:unsorted GO:query 659s @SQ SN:0 LN:19 659s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" 659s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 659s Fastq 4 (fw:1, sam:1) 659s References: 659s >0 659s AGCATCGATCAGTATCTGA 659s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz 659s Error: Read r0 has more read characters than quality values. 659s terminate called after throwing an instance of 'int' 660s Aborted (core dumped) 660s (ERR): bowtie2-align exited with value 134 660s Fastq 5 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAGTATCTGA 660s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz 660s Error: Read r0 has more read characters than quality values. 660s terminate called after throwing an instance of 'int' 660s Aborted (core dumped) 660s (ERR): bowtie2-align exited with value 134 660s Fastq 6 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAGTATCTGA 660s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz 660s Error: reads file does not look like a FASTQ file 660s terminate called after throwing an instance of 'int' 660s Aborted (core dumped) 660s (ERR): bowtie2-align exited with value 134 660s Fastq 7 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAGTATCTGA 660s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:19 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz" 660s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 660s Fastq 8 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAGTATCTGA 660s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:19 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" 660s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 660s Fastq 9 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAGTATCTGA 660s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:19 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" 660s Fastq multiread 1 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAGTATCTGA 660s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:19 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" 660s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 660s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 660s Fastq multiread 2 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAGTATCTGA 660s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:19 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" 660s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 660s Fastq multiread 3 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAGTATCTGA 660s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz 660s @HD VN:1.5 SO:unsorted GO:query 660s @SQ SN:0 LN:19 660s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" 660s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 660s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 660s Fastq paired 1 (fw:1, sam:1) 660s References: 660s >0 660s AGCATCGATCAAAAACTGA 660s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 661s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:19 661s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 661s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 661s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 661s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 661s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 661s Fastq paired 2 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAAAAACTGA 661s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:19 661s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 661s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 661s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 661s Fastq paired 3 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAAAAACTGA 661s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:19 661s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 661s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 661s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 661s Fastq paired 4 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAAAAACTGA 661s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:19 661s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 661s r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 661s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 661s Fasta 1 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAGTATCTGA 661s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 661s /usr/bin/bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:19 661s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" 661s r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 661s Fasta 2 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAGTATCTGA 661s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:19 661s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz" 661s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 661s Fasta 3 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAGTATCTGA 661s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz 661s @HD VN:1.5 SO:unsorted GO:query 661s @SQ SN:0 LN:19 661s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" 661s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 661s Fasta 5 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAGTATCTGA 661s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz 661s Error: reads file does not look like a FASTA file 661s terminate called after throwing an instance of 'int' 661s Aborted (core dumped) 661s (ERR): bowtie2-align exited with value 134 661s Fasta 6 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAGTATCTGA 661s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz 661s Error: reads file does not look like a FASTA file 661s terminate called after throwing an instance of 'int' 661s Aborted (core dumped) 661s (ERR): bowtie2-align exited with value 134 661s Fasta 7 (fw:1, sam:1) 661s References: 661s >0 661s AGCATCGATCAGTATCTGA 661s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 662s Fasta 8 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 662s Fasta 9 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s Fasta multiread 1 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 662s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 662s Fasta multiread 2 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 662s Fasta multiread 3 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 662s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 662s Fasta multiline 1 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 662s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 662s Fasta multiline 2 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 662s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 662s Fasta multiline 3 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" 662s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 662s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 662s Fasta paired 1 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAAAAACTGA 662s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 662s /usr/bin/bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 662s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 662s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 662s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 662s r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP 662s Fasta paired 2 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAAAAACTGA 662s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 662s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 662s r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP 662s Fasta paired 3 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAAAAACTGA 662s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 662s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 662s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 662s Fasta paired 4 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAAAAACTGA 662s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 662s @HD VN:1.5 SO:unsorted GO:query 662s @SQ SN:0 LN:19 662s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 662s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 662s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 662s Raw 1 (fw:1, sam:1) 662s References: 662s >0 662s AGCATCGATCAGTATCTGA 662s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 663s /usr/bin/bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 663s Raw 2 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 663s Raw 3 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 663s Raw 7 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 663s Raw 8 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 663s Raw 9 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s Raw multiread 1 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 663s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 663s Raw multiread 2 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 663s Raw multiread 3 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" 663s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 663s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 663s Raw paired 1 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAAAAACTGA 663s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 663s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 663s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 663s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 663s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 663s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 663s Raw paired 2 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAAAAACTGA 663s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 663s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 663s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 663s Raw paired 3 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAAAAACTGA 663s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 663s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 663s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 663s Raw paired 4 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAAAAACTGA 663s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 663s @HD VN:1.5 SO:unsorted GO:query 663s @SQ SN:0 LN:19 663s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 663s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 663s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 663s Tabbed 1 (fw:1, sam:1) 663s References: 663s >0 663s AGCATCGATCAGTATCTGA 663s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 664s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:19 664s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 664s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 664s Tabbed 2 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:19 664s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 664s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 664s Tabbed 3 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:19 664s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 664s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 664s Tabbed 4 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s Error: Read r0 has more read characters than quality values. 664s terminate called after throwing an instance of 'int' 664s Aborted (core dumped) 664s (ERR): bowtie2-align exited with value 134 664s Tabbed 5 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s Error: Read r0 has more quality values than read characters. 664s terminate called after throwing an instance of 'int' 664s Aborted (core dumped) 664s (ERR): bowtie2-align exited with value 134 664s Tabbed 7 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:19 664s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 664s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 664s Tabbed 8 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:19 664s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 664s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 664s Tabbed 9 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:19 664s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 664s Tabbed multiread 1 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:19 664s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 664s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 664s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 664s Tabbed multiread 2 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 664s @HD VN:1.5 SO:unsorted GO:query 664s @SQ SN:0 LN:19 664s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 664s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 664s Tabbed multiread 3 (fw:1, sam:1) 664s References: 664s >0 664s AGCATCGATCAGTATCTGA 664s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 665s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 665s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 665s Tabbed paired 1 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAAAAACTGA 665s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 665s /usr/bin/bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 665s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 665s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 665s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 665s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 665s Tabbed paired 2 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAAAAACTGA 665s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 665s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 665s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 665s Tabbed paired 3 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAAAAACTGA 665s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 665s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 665s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 665s Tabbed paired 4 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAAAAACTGA 665s /usr/bin/bowtie2 -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 665s r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 665s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 665s Qseq 1 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAGTATCTGA 665s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 665s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 665s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 665s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 665s Qseq 2 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAGTATCTGA 665s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 665s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 665s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 665s Qseq 3 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAGTATCTGA 665s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 665s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 665s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 665s Qseq 4 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAGTATCTGA 665s /usr/bin/bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 665s Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. 665s terminate called after throwing an instance of 'int' 665s Aborted (core dumped) 665s Qseq 7 (fw:1, sam:1) 665s References: 665s >0 665s (ERR): bowtie2-align exited with value 134 665s AGCATCGATCAGTATCTGA 665s /usr/bin/bowtie2 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 665s @HD VN:1.5 SO:unsorted GO:query 665s @SQ SN:0 LN:19 665s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 665s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 665s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 665s Qseq 8 (fw:1, sam:1) 665s References: 665s >0 665s AGCATCGATCAGTATCTGA 665s /usr/bin/bowtie2 --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:19 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 666s MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 666s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 666s Qseq 9 (fw:1, sam:1) 666s References: 666s >0 666s AGCATCGATCAGTATCTGA 666s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:19 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 666s Qseq multiread 1 (fw:1, sam:1) 666s References: 666s >0 666s AGCATCGATCAGTATCTGA 666s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:19 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 666s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 666s MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 666s Qseq multiread 2 (fw:1, sam:1) 666s References: 666s >0 666s AGCATCGATCAGTATCTGA 666s /usr/bin/bowtie2 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:19 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 666s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 666s Qseq multiread 3 (fw:1, sam:1) 666s References: 666s >0 666s AGCATCGATCAGTATCTGA 666s /usr/bin/bowtie2 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:19 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 666s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 666s MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 666s Qseq paired 1 (fw:1, sam:1) 666s References: 666s >0 666s AGCATCGATCAAAAACTGA 666s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 666s /usr/bin/bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:19 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 666s MachName_RunNum_Lane_Tile_10_10_Index 99 0 1 255 10M = 9 19 AGCATCGATC ABCBGACBCB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 666s MachName_RunNum_Lane_Tile_10_10_Index 147 0 9 255 11M = 1 -19 TCAAAAACTGA ABCBCAGBCBA AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 666s MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 666s MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 666s Qseq paired 2 (fw:1, sam:1) 666s References: 666s >0 666s AGCATCGATCAAAAACTGA 666s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:19 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 666s MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 666s MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 666s Left-align insertion (fw:1, sam:1) 666s References: 666s >0 666s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 666s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 666s /usr/bin/bowtie2 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:73 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 666s r0 0 0 23 24 2M1I40M * 0 0 ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:42 YT:Z:UU 666s Left-align deletion (fw:1, sam:1) 666s References: 666s >0 666s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 666s /usr/bin/bowtie2 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:73 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 666s r0 0 0 19 40 6M1D39M * 0 0 ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^A39 YT:Z:UU 666s Left-align insertion with mismatch at LHS (fw:1, sam:1) 666s References: 666s >0 666s GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 666s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 666s /usr/bin/bowtie2 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 666s @HD VN:1.5 SO:unsorted GO:query 666s @SQ SN:0 LN:73 666s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 666s r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU 666s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 666s References: 666s >0 666s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 666s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:1192 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 669s r0 65 0 3 42 38M = 1148 0 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UP 669s r0 129 0 1148 1 42M = 3 0 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UP 669s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 669s References: 669s >0 669s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:1028 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 669s r0 65 0 3 42 38M = 982 1021 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:DP 669s r0 129 0 982 42 42M = 3 -1021 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:DP 669s MREVERSE flag is set if mate does not align (fw:1, sam:1) 669s References: 669s >0 669s TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:250 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 669s r0 89 0 51 42 100M = 51 0 TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP 669s r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 669s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 669s References: 669s >0 669s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --fr --quiet --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:290 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 669s r0 99 0 3 1 38M = 246 285 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:CP 669s r0 147 0 246 1 42M = 3 -285 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:CP 669s MD:Z 1 (fw:1, sam:1) 669s References: 669s >0 669s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:54 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU 669s MD:Z 1 (fw:0, sam:1) 669s References: 669s >0 669s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 669s /usr/bin/bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:54 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU 669s MD:Z 2 (fw:1, sam:1) 669s References: 669s >0 669s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:54 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU 669s MD:Z 2 (fw:0, sam:1) 669s References: 669s >0 669s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 669s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:54 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU 669s MD:Z 3 (fw:1, sam:1) 669s References: 669s >0 669s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:55 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU 669s MD:Z 3 (fw:0, sam:1) 669s References: 669s >0 669s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 669s /usr/bin/bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:55 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU 669s MD:Z 4 (fw:1, sam:1) 669s References: 669s >0 669s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:55 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU 669s MD:Z 4 (fw:0, sam:1) 669s References: 669s >0 669s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 669s /usr/bin/bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:55 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU 669s Local alignment 1 (fw:1, sam:1) 669s References: 669s >0 669s TTGT 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:4 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU 669s Local alignment 1 (fw:0, sam:1) 669s References: 669s >0 669s TTGT 669s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:4 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU 669s Local alignment 2 (fw:1, sam:1) 669s References: 669s >0 669s TTGA 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:4 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 669s Local alignment 2 (fw:0, sam:1) 669s References: 669s >0 669s TTGA 669s /usr/bin/bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:4 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 669s Local alignment 3 (fw:1, sam:1) 669s References: 669s >0 669s TTGTTCGTTTGTTCGT 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:16 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 669s r0 256 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 669s Local alignment 3 (fw:0, sam:1) 669s References: 669s >0 669s TTGTTCGTTTGTTCGT 669s /usr/bin/bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:16 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 669s r0 272 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 669s Local alignment 4 (fw:1, sam:1) 669s References: 669s >0 669s TTGTTCGTTTGTTCGT 669s /usr/bin/bowtie2 --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:16 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 669s r0 256 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 669s Local alignment 4 (fw:0, sam:1) 669s References: 669s >0 669s TTGTTCGTTTGTTCGT 669s /usr/bin/bowtie2 --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:16 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 669s r0 272 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 669s Alignment order -k (fw:1, sam:1) 669s References: 669s >0 669s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 669s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 669s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:86 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 669s r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 669s r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 669s r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 669s Alignment order -k (fw:0, sam:1) 669s References: 669s >0 669s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 669s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 669s @HD VN:1.5 SO:unsorted GO:query 669s @SQ SN:0 LN:86 669s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 669s r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 669s r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 669s r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 669s r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 669s Alignment order -a (fw:1, sam:1) 669s References: 669s >0 669s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 669s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:86 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 670s r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 670s r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 670s r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 670s r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 670s Alignment order -a (fw:0, sam:1) 670s References: 670s >0 670s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 670s /usr/bin/bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:86 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 670s r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 670s r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 670s r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 670s r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 670s Mate reporting order, -a (fw:1, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 670s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 670s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:407 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 670s r0 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r2 99 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 670s r2 147 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 670s Mate reporting order, -a (fw:0, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 670s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:407 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 670s r0 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r2 83 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 670s r2 163 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 670s Mate reporting order, -M 1 (fw:1, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 670s /usr/bin/bowtie2 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:407 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 670s r0 99 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 147 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 83 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 163 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r2 99 0 307 42 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 670s r2 147 0 379 42 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 670s Mate reporting order, -M 1 (fw:0, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 670s /usr/bin/bowtie2 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:407 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 670s r0 83 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 163 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 99 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r1 147 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r2 83 0 379 42 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 670s r2 163 0 307 42 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 670s Non-overlapping; no args (fw:1, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 670s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 670s /usr/bin/bowtie2 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:47 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 670s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 670s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s Non-overlapping; no args (fw:0, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 670s /usr/bin/bowtie2 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:47 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 670s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 670s Non-overlapping; --no-discordant (fw:1, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 670s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:47 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 670s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 670s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s Non-overlapping; --no-discordant (fw:0, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 670s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:47 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 670s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 670s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:47 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 670s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 670s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 670s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:47 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 670s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 670s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 670s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 670s @HD VN:1.5 SO:unsorted GO:query 670s @SQ SN:0 LN:47 670s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 670s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 670s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 670s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 670s References: 670s >0 670s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 670s /usr/bin/bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 670s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 671s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 671s Non-overlapping; --no-dovetail (fw:1, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 671s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 671s Non-overlapping; --no-dovetail (fw:0, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 671s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 671s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 671s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 671s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 671s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 671s Non-overlapping; --no-overlap (fw:1, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 671s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 671s Non-overlapping; --no-overlap (fw:0, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 671s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 671s Overlapping; no args (fw:1, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 671s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 671s Overlapping; no args (fw:0, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 671s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 671s Overlapping; --no-dovetail (fw:1, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 671s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 671s Overlapping; --no-dovetail (fw:0, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 671s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 671s Overlapping; --no-contain (fw:1, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-contain --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 671s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 671s Overlapping; --no-contain (fw:0, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-contain --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 671s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 671s Overlapping; --no-overlap (fw:1, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 65 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 671s r0 129 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP 671s Overlapping; --no-overlap (fw:0, sam:1) 671s References: 671s >0 671s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 671s /usr/bin/bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 671s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 671s @HD VN:1.5 SO:unsorted GO:query 671s @SQ SN:0 LN:47 671s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 671s r0 113 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP 671s r0 177 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 671s Scoring params 1 (fw:1, sam:1) 671s References: 671s >0 671s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 671s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 671s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:105 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 0 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU 672s Scoring params 1 (fw:0, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:105 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 16 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU 672s Scoring params 2 (fw:1, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 672s /usr/bin/bowtie2 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 2 (fw:0, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 3 (fw:1, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 3 (fw:0, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 4 (fw:1, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 4 (fw:0, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 5 (fw:1, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 5 (fw:0, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 6 (fw:1, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Scoring params 6 (fw:0, sam:1) 672s References: 672s >0 672s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 672s /usr/bin/bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 672s @HD VN:1.5 SO:unsorted GO:query 672s @SQ SN:0 LN:102 672s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 672s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 672s Q XS:i 1a (fw:1, sam:1) 672s References: 672s >0 672s TTGTTCGATTGTTCGA 672s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 672s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 672s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a ! --mp 3,6 (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s Q XS:i 1a ! --mp 3,6 (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a I --mp 3,3 (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a I --mp 3,3 (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a I --mp 3,6 (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a I --mp 3,6 (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a --ignore-quals (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1a --ignore-quals (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1b (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1b (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1b --ignore-quals (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1b --ignore-quals (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1c (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1c (fw:0, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 673s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 673s @HD VN:1.5 SO:unsorted GO:query 673s @SQ SN:0 LN:16 673s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 673s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 673s Q XS:i 1c --ignore-quals (fw:1, sam:1) 673s References: 673s >0 673s TTGTTCGATTGTTCGA 673s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:16 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 674s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 674s Q XS:i 1c --ignore-quals (fw:0, sam:1) 674s References: 674s >0 674s TTGTTCGATTGTTCGA 674s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:16 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 674s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 674s (fw:1, sam:1) 674s References: 674s >0 674s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 674s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 674s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:68 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 674s r0 73 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP 674s r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 674s (fw:0, sam:1) 674s References: 674s >0 674s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 674s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:68 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 674s r0 137 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP 674s r0 69 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 674s (fw:1, sam:1) 674s References: 674s >0 674s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 674s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 674s /usr/bin/bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:528 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 674s r0 0 0 217 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 674s (fw:0, sam:1) 674s References: 674s >0 674s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 674s /usr/bin/bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:528 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 674s r0 16 0 89 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 674s (fw:1, sam:1) 674s References: 674s >0 674s TTGTTCGTTTGTTCGT 674s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 674s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:16 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 674s r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 674s (fw:0, sam:1) 674s References: 674s >0 674s TTGTTCGTTTGTTCGT 674s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:16 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 674s r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 674s (fw:1, sam:1) 674s References: 674s >0 674s TTGTTCGTTTGTTCGT 674s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:16 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 674s r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 674s (fw:0, sam:1) 674s References: 674s >0 674s TTGTTCGTTTGTTCGT 674s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 674s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 674s @HD VN:1.5 SO:unsorted GO:query 674s @SQ SN:0 LN:16 674s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 674s r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 674s XS:i 1 (fw:1, sam:1) 674s References: 674s >0 674s TTGTTCGATTGTTCGA 674s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 675s XS:i 1 (fw:0, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGA 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 675s XS:i 2 (fw:1, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGA 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU 675s XS:i 2 (fw:0, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGA 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU 675s XS:i 3a (fw:1, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGT 675s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 675s XS:i 3a (fw:0, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGT 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 675s XS:i 3b (fw:1, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGT 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 675s XS:i 3b (fw:0, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGT 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 675s XS:i 3c (fw:1, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGT 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 675s XS:i 3c (fw:0, sam:1) 675s References: 675s >0 675s TTGTTCGATTGTTCGT 675s /usr/bin/bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 675s @HD VN:1.5 SO:unsorted GO:query 675s @SQ SN:0 LN:16 675s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 675s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 675s XS:i 4a (fw:1, sam:1) 675s References: 675s >0 675s TTGTTCAATTGTTCGATTGTTCGT 675s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 675s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 675s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:24 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 676s XS:i 4a (fw:0, sam:1) 676s References: 676s >0 676s TTGTTCAATTGTTCGATTGTTCGT 676s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:24 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 676s XS:i 4b (fw:1, sam:1) 676s References: 676s >0 676s TTGTTCAATTGTTCGATTGTTCGT 676s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:24 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 676s XS:i 4b (fw:0, sam:1) 676s References: 676s >0 676s TTGTTCAATTGTTCGATTGTTCGT 676s /usr/bin/bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:24 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 676s XS:i 5a (fw:1, sam:1) 676s References: 676s >0 676s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 676s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 676s /usr/bin/bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:120 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 676s XS:i 5a (fw:0, sam:1) 676s References: 676s >0 676s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 676s /usr/bin/bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:120 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 676s XS:i 5b (fw:1, sam:1) 676s References: 676s >0 676s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 676s /usr/bin/bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:120 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 676s XS:i 5b (fw:0, sam:1) 676s References: 676s >0 676s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 676s /usr/bin/bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:120 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 676s BWA-SW-like 1 (fw:1, sam:1) 676s References: 676s >0 676s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 676s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 676s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 676s /usr/bin/bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:64 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU 676s BWA-SW-like 1 (fw:0, sam:1) 676s References: 676s >0 676s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 676s /usr/bin/bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:64 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU 676s BWA-SW-like 2 (fw:1, sam:1) 676s References: 676s >0 676s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 676s /usr/bin/bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:64 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU 676s BWA-SW-like 2 (fw:0, sam:1) 676s References: 676s >0 676s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 676s /usr/bin/bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:64 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU 676s BWA-SW-like 3 (fw:1, sam:1) 676s References: 676s >0 676s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 676s /usr/bin/bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 676s @HD VN:1.5 SO:unsorted GO:query 676s @SQ SN:0 LN:64 676s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 676s r0 0 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU 676s BWA-SW-like 3 (fw:0, sam:1) 676s References: 676s >0 676s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 676s /usr/bin/bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:64 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 677s r0 16 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU 677s SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 677s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 99 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 677s r0 147 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 677s SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 67 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 677s r0 131 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 677s SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2 --rf --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 83 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 677s r0 163 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 677s SAM paired-end where both mates align 1 (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 99 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 677s r0 147 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 677s SAM paired-end where both mates align 2 (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2 --rf --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 83 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 677s r0 163 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 677s SAM paired-end where both mates align 3 (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 67 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 677s r0 131 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 677s SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 73 0 4 255 24M = 4 0 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YT:Z:UP 677s r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 677s SAM paired-end where neither mate aligns (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 677s r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 677s SAM paired-end where both mates align, but discordantly (fw:1, sam:1) 677s References: 677s >0 677s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 677s /usr/bin/bowtie2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:69 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 677s r0 65 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YS:i:0 YT:Z:DP 677s r0 129 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 677s matchesRef regression 4 (fw:1, sam:1) 677s References: 677s >0 677s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 677s >1 677s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 677s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 677s /usr/bin/bowtie2 --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:120 677s @SQ SN:1 LN:31 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 677s r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 677s matchesRef regression 4 (fw:0, sam:1) 677s References: 677s >0 677s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 677s >1 677s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 677s /usr/bin/bowtie2 --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 677s @HD VN:1.5 SO:unsorted GO:query 677s @SQ SN:0 LN:120 677s @SQ SN:1 LN:31 677s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 677s r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 677s matchesRef regression 3 (fw:1, sam:1) 677s References: 677s >0 677s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 677s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 678s /usr/bin/bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 678s @HD VN:1.5 SO:unsorted GO:query 678s @SQ SN:0 LN:53 678s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 678s r0 16 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU 678s matchesRef regression 3 (fw:0, sam:1) 678s References: 678s >0 678s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 678s /usr/bin/bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 678s @HD VN:1.5 SO:unsorted GO:query 678s @SQ SN:0 LN:53 678s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 678s r0 0 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU 678s matchesRef regression 2 (fw:1, sam:1) 678s References: 678s >0 678s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 678s >1 678s CCTTGTTNTTAATGCTGCCTGGTTTNG 678s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 678s /usr/bin/bowtie2 --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 678s @HD VN:1.5 SO:unsorted GO:query 678s @SQ SN:0 LN:47 678s @SQ SN:1 LN:27 678s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 678s r0 77 * 0 0 * * 0 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 678s r0 141 * 0 0 * * 0 0 ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 678s matchesRef regression 2 (fw:0, sam:1) 678s References: 678s >0 678s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 678s >1 678s CCTTGTTNTTAATGCTGCCTGGTTTNG 678s /usr/bin/bowtie2 --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 678s @HD VN:1.5 SO:unsorted GO:query 678s @SQ SN:0 LN:47 678s @SQ SN:1 LN:27 678s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 678s r0 83 0 1 255 29S23M = 1 -68 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:-128 YT:Z:CP 678s r0 163 0 1 255 45S15M = 1 68 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-128 XN:i:9 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:14T0 YS:i:-78 YT:Z:CP 678s matchesRef regression 1 (fw:1, sam:1) 678s References: 678s >0 678s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 678s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 678s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 678s @HD VN:1.5 SO:unsorted GO:query 678s @SQ SN:0 LN:61 678s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 678s r0 0 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU 678s matchesRef regression 1 (fw:0, sam:1) 678s References: 678s >0 678s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 678s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 678s @HD VN:1.5 SO:unsorted GO:query 678s @SQ SN:0 LN:61 678s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 678s r0 16 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU 678s Discordant with different chromosomes (fw:1, sam:1) 678s References: 678s >0 678s TTTATAAAAATATTTCCCCCCCC 678s >1 678s CCCCCCTGTCGCTACCGCCCCCCCCCCC 678s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 678s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 678s @HD VN:1.5 SO:unsorted GO:query 678s @SQ SN:0 LN:23 678s @SQ SN:1 LN:28 678s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 678s r0 65 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 678s r0 129 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 678s r1 65 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 678s r1 129 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 678s Discordant with different chromosomes (fw:0, sam:1) 678s References: 678s >0 678s TTTATAAAAATATTTCCCCCCCC 678s >1 678s CCCCCCTGTCGCTACCGCCCCCCCCCCC 678s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:23 679s @SQ SN:1 LN:28 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 679s r0 113 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 679s r0 177 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 679s r1 113 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 679s r1 177 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 679s (fw:1, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 679s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 679s r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 679s (fw:0, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 679s r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 679s (fw:1, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 679s r1 99 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 679s r1 147 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 679s (fw:0, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 679s r1 83 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 679s r1 163 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 679s (fw:1, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 679s (fw:0, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 679s (fw:1, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 2 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 679s (fw:0, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 2 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 679s (fw:1, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 679s r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 679s (fw:0, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 679s r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 679s (fw:1, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 679s r1 0 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 679s (fw:0, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 679s r1 16 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 679s (fw:0, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 --trim5 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 679s r1 16 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 679s (fw:1, sam:1) 679s References: 679s >0 679s AGCATCGATCAGTATCTGA 679s /usr/bin/bowtie2 -s 1 --trim5 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 679s @HD VN:1.5 SO:unsorted GO:query 679s @SQ SN:0 LN:19 679s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 679s r1 0 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 679s (fw:1, sam:1) 679s References: 679s >0 679s TGC 679s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 680s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:3 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 680s r0 0 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 680s (fw:0, sam:1) 680s References: 680s >0 680s TGC 680s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:3 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 680s r0 16 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 680s (fw:1, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 680s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 680s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s (fw:0, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 680s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s (fw:1, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 680s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s (fw:0, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 680s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s (fw:1, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 680s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s (fw:0, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 680s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s (fw:1, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 680s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s (fw:0, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 680s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s (fw:1, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 680s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s r1 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 680s r2 0 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 680s (fw:0, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 680s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s r1 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 680s r2 16 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 680s (fw:1, sam:1) 680s References: 680s >0 680s TTGTTCGT 680s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 680s @HD VN:1.5 SO:unsorted GO:query 680s @SQ SN:0 LN:8 680s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 680s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 680s r2 4 * 0 0 * * 0 0 GTTCGTA IIIIIII YT:Z:UU 680s r3 4 * 0 0 * * 0 0 ATTGTTC IIIIIII YT:Z:UU 680s (fw:0, sam:1) 680s References: 680s >0 680s TTGTTCGT 681s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:8 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 681s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 681s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 681s r2 4 * 0 0 * * 0 0 TACGAAC IIIIIII YT:Z:UU 681s r3 4 * 0 0 * * 0 0 GAACAAT IIIIIII YT:Z:UU 681s (fw:1, sam:1) 681s References: 681s >0 681s TTGTTCGT 681s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:8 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 681s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 681s (fw:0, sam:1) 681s References: 681s >0 681s TTGTTCGT 681s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:8 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 681s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 681s (fw:1, sam:1) 681s References: 681s >0 681s TTGTTCGT 681s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:8 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 681s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 681s (fw:0, sam:1) 681s References: 681s >0 681s TTGTTCGT 681s /usr/bin/bowtie2 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:8 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 681s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 681s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 681s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 681s /usr/bin/bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 681s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:1000 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 681s r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 681s /usr/bin/bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 681s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:1000 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 681s r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 681s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 681s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:1000 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 681s r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 681s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 681s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:1000 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 681s r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 681s /usr/bin/bowtie2 -X 1000 --fr --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:1000 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 681s r0 99 0 13 1 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 147 0 553 1 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 355 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 403 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 355 0 13 255 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 403 0 790 255 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 355 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 403 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 355 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 403 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 681s /usr/bin/bowtie2 -X 1000 --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:1000 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 681s r0 83 0 553 1 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 163 0 13 1 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 419 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 339 0 790 255 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 419 0 13 255 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 339 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 419 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s r0 339 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 681s r0 419 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 681s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 681s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:1000 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 681s r0 99 0 13 1 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 147 0 553 1 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 355 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 403 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 355 0 13 255 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 403 0 790 255 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 355 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 403 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 355 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 403 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 681s /usr/bin/bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 681s @HD VN:1.5 SO:unsorted GO:query 681s @SQ SN:0 LN:1000 681s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 681s r0 83 0 553 1 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 163 0 13 1 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 419 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 339 0 790 255 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 419 0 13 255 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 339 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 419 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s r0 339 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 681s r0 419 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 681s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 681s References: 681s >0 681s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 681s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 682s /usr/bin/bowtie2 -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 682s r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 682s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 -X 150 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 682s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 682s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 682s r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 682s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --local -X 150 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 682s r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 682s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 682s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 682s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 682s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 682s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 682s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 682s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 682s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 682s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 682s r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 682s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 682s r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 682s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 682s r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 682s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:363 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 682s r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 682s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 682s /usr/bin/bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 682s @HD VN:1.5 SO:unsorted GO:query 682s @SQ SN:0 LN:126 682s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 682s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 682s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 682s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 682s References: 682s >0 682s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 682s /usr/bin/bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:126 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 683s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 683s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 683s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:126 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 683s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 683s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 683s /usr/bin/bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:126 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 683s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 683s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 683s /usr/bin/bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:126 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 99 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 683s r0 147 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 683s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 683s /usr/bin/bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:126 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 83 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 683s r0 163 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 683s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 683s /usr/bin/bowtie2 -X 150 --local --fr --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:126 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 99 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 683s r0 147 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 683s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 683s /usr/bin/bowtie2 -X 150 --local --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:126 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 83 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 683s r0 163 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 683s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 683s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 683s /usr/bin/bowtie2 -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:2607 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 99 0 1435 1 33M = 1501 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 683s r0 147 0 1501 1 28M = 1435 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 683s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 683s /usr/bin/bowtie2 -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:2607 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 83 0 790 1 28M = 724 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 683s r0 163 0 724 1 33M = 790 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 683s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 683s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 683s /usr/bin/bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:1906 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 683s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 683s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 683s /usr/bin/bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 683s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 683s @HD VN:1.5 SO:unsorted GO:query 683s @SQ SN:0 LN:1906 683s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 683s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 683s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 683s U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1) 683s References: 683s >0 683s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 683s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 684s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:56 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 0 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 684s U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) 684s References: 684s >0 684s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 684s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:56 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 16 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 684s U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) 684s References: 684s >0 684s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 684s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:56 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 0 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 684s U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1) 684s References: 684s >0 684s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 684s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:56 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 16 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 684s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1) 684s References: 684s >0 684s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 684s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:56 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 684s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1) 684s References: 684s >0 684s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 684s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:56 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 684s U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1) 684s References: 684s >0 684s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 684s /usr/bin/bowtie2 --local --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:56 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 684s U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1) 684s References: 684s >0 684s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 684s /usr/bin/bowtie2 --local --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:56 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 684s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) 684s References: 684s >0 684s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 684s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 684s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:85 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 684s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) 684s References: 684s >0 684s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 684s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:85 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 684s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) 684s References: 684s >0 684s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 684s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:85 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 684s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) 684s References: 684s >0 684s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 684s /usr/bin/bowtie2 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:85 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 684s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1) 684s References: 684s >0 684s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 684s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 684s @HD VN:1.5 SO:unsorted GO:query 684s @SQ SN:0 LN:85 684s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 684s r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 684s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) 684s References: 684s >0 684s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 684s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --quiet -M 2 --local --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --quiet -k 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --quiet -k 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --local --quiet -k 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:85 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 685s /usr/bin/bowtie2 -X 150 --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:340 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 0 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:340 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 685s References: 685s >0 685s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 685s /usr/bin/bowtie2 --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 685s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 685s @HD VN:1.5 SO:unsorted GO:query 685s @SQ SN:0 LN:340 685s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 685s r0 0 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 685s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 685s References: 685s >0 686s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 686s /usr/bin/bowtie2 --local --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:340 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) 686s References: 686s >0 686s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 686s /usr/bin/bowtie2 --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:340 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 0 0 304 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 256 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 256 0 219 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1) 686s References: 686s >0 686s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 686s /usr/bin/bowtie2 --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:340 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 272 0 219 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1) 686s References: 686s >0 686s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 686s /usr/bin/bowtie2 --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:340 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 0 0 304 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 256 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 256 0 219 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1) 686s References: 686s >0 686s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 686s /usr/bin/bowtie2 --local --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:340 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s r0 272 0 219 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 686s (fw:1, sam:1) 686s References: 686s >0 686s TTGTTCGTTTGTTCGT 686s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 686s /usr/bin/bowtie2 -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:16 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 0 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 686s r0 256 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 686s (fw:0, sam:1) 686s References: 686s >0 686s TTGTTCGTTTGTTCGT 686s /usr/bin/bowtie2 -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:16 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 16 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 686s r0 272 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 686s (fw:1, sam:1) 686s References: 686s >0 686s TTGTTCGTTTGTTCGT 686s /usr/bin/bowtie2 -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:16 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 4 * 0 0 * * 0 0 TTGTTCAT IIIIIIII YT:Z:UU 686s (fw:0, sam:1) 686s References: 686s >0 686s TTGTTCGTTTGTTCGT 686s /usr/bin/bowtie2 -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:16 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 686s r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU 686s (fw:1, sam:1) 686s References: 686s >0 686s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 686s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 686s /usr/bin/bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:49 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 686s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s (fw:0, sam:1) 686s References: 686s >0 686s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 686s /usr/bin/bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 686s @HD VN:1.5 SO:unsorted GO:query 686s @SQ SN:0 LN:49 686s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 686s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 686s Gap penalties 1 (fw:1, sam:1) 686s References: 686s >0 686s TTGTTCGTTTGTTCGT 686s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 0 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU 687s Gap penalties 1 (fw:0, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 16 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU 687s Gap penalties 2 (fw:1, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 4 * 0 0 * * 0 0 TTGTTCTTTGTT IIIIIIIIIIII YT:Z:UU 687s Gap penalties 2 (fw:0, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 4 * 0 0 * * 0 0 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU 687s Gap penalties 3 (fw:1, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 687s Gap penalties 3 (fw:0, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 687s Gap penalties 4 (fw:1, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 687s Gap penalties 4 (fw:0, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 687s Gap penalties 5 (fw:1, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 687s Gap penalties 5 (fw:0, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:16 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 687s Gap penalties 6 (fw:1, sam:1) 687s References: 687s >0 687s ATTGTTCGTTTGTTCGTA 687s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:18 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 0 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU 687s Gap penalties 6 (fw:0, sam:1) 687s References: 687s >0 687s ATTGTTCGTTTGTTCGTA 687s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 687s @HD VN:1.5 SO:unsorted GO:query 687s @SQ SN:0 LN:18 687s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 687s r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU 687s Gap penalties 7 (fw:1, sam:1) 687s References: 687s >0 687s TTGTTCGTTTGTTCGT 687s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 688s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:16 688s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 688s r0 4 * 0 0 * * 0 0 TTGTTGTTTGATTCGT IIIIIIIIIIIIIIII YT:Z:UU 688s Gap penalties 7 (fw:0, sam:1) 688s References: 688s >0 688s TTGTTCGTTTGTTCGT 688s /usr/bin/bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:16 688s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 688s r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU 688s N filtering 1 (fw:1, sam:1) 688s References: 688s >0 688s GAGACTTTATACGCATCGAACTATCGCTCTA 688s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 688s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:31 688s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 688s r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 688s N filtering 1 (fw:0, sam:1) 688s References: 688s >0 688s GAGACTTTATACGCATCGAACTATCGCTCTA 688s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:31 688s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 688s r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 688s N filtering 2 (fw:1, sam:1) 688s References: 688s >0 688s GAGACTTTATNCGCATCGAACTATCGCTCTA 688s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 688s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:31 688s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 688s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 688s N filtering 2 (fw:0, sam:1) 688s References: 688s >0 688s GAGACTTTATNCGCATCGAACTATCGCTCTA 688s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:31 688s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 688s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 688s N filtering 3 (fw:1, sam:1) 688s References: 688s >0 688s GAGACTTTATACGCATCGAANTATCGCTCTA 688s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 688s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:31 688s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 688s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 688s N filtering 3 (fw:0, sam:1) 688s References: 688s >0 688s GAGACTTTATACGCATCGAANTATCGCTCTA 688s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 688s @HD VN:1.5 SO:unsorted GO:query 688s @SQ SN:0 LN:31 688s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 688s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 688s N filtering 4 (fw:1, sam:1) 688s References: 688s >0 688s GAGACTTTNTACGCATCGAACTATCGCTCTA 688s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 689s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:31 689s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 689s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 689s N filtering 4 (fw:0, sam:1) 689s References: 689s >0 689s GAGACTTTNTACGCATCGAACTATCGCTCTA 689s /usr/bin/bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:31 689s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 689s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 689s N filtering 5 (fw:1, sam:1) 689s References: 689s >0 689s GAGACTTTATNCGCATCGAACTATCGCTCTA 689s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 689s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:31 689s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 689s r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU 689s N filtering 5 (fw:0, sam:1) 689s References: 689s >0 689s GAGACTTTATNCGCATCGAACTATCGCTCTA 689s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:31 689s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 689s r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU 689s N filtering 6 (fw:1, sam:1) 689s References: 689s >0 689s GAGACTTTNTACGCATCGAANTATCGCTCTA 689s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 689s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:31 689s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 689s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 689s N filtering 6 (fw:0, sam:1) 689s References: 689s >0 689s GAGACTTTNTACGCATCGAANTATCGCTCTA 689s /usr/bin/bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:31 689s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 689s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 689s (fw:1, sam:1) 689s References: 689s >0 689s TTTTGTTCGTTTG 689s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 689s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:13 689s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 689s r0 0 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 689s (fw:0, sam:1) 689s References: 689s >0 689s TTTTGTTCGTTTG 689s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 689s @HD VN:1.5 SO:unsorted GO:query 689s @SQ SN:0 LN:13 689s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 689s r0 16 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 689s (fw:1, sam:1) 689s References: 689s >0 689s TTGTTCGTTTGTT 689s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 690s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:13 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 690s r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 690s (fw:0, sam:1) 690s References: 690s >0 690s TTGTTCGTTTGTT 690s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:13 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 690s r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 690s (fw:1, sam:1) 690s References: 690s >0 690s ACNCA 690s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 690s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:5 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 690s r0 0 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s (fw:0, sam:1) 690s References: 690s >0 690s ACNCA 690s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:5 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 690s r0 16 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s N ceil = 0, 2 legit hits (1) (fw:1, sam:1) 690s References: 690s >0 690s ACNCA 690s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:5 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 690s r0 0 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s N ceil = 0, 2 legit hits (1) (fw:0, sam:1) 690s References: 690s >0 690s ACNCA 690s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:5 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 690s r0 16 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s N ceil = 0, 2 legit hits (2) (fw:1, sam:1) 690s References: 690s >0 690s ACNCANNNNNNNNCGNNNNNNNNCG 690s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 690s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:25 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 690s r0 0 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s N ceil = 0, 2 legit hits (2) (fw:0, sam:1) 690s References: 690s >0 690s ACNCANNNNNNNNCGNNNNNNNNCG 690s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 690s @HD VN:1.5 SO:unsorted GO:query 690s @SQ SN:0 LN:25 690s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 690s r0 0 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 690s (fw:1, sam:1) 690s References: 690s >0 690s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 690s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 690s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:37 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 691s r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s (fw:0, sam:1) 691s References: 691s >0 691s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 691s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:37 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 691s r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s (fw:1, sam:1) 691s References: 691s >0 691s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 691s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:37 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 691s r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s (fw:0, sam:1) 691s References: 691s >0 691s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 691s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:37 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 691s r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 691s (fw:1, sam:1) 691s References: 691s >0 691s TTGTTYGT 691s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 691s /usr/bin/bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:8 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 691s r0 0 0 1 255 8M * 0 0 TTGTTGGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU 691s r1 0 0 1 255 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU 691s (fw:1, sam:1) 691s References: 691s >0 691s ATAACCTTCG 691s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 691s /usr/bin/bowtie2 --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:10 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 691s r0 0 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU 691s (fw:0, sam:1) 691s References: 691s >0 691s ATAACCTTCG 691s /usr/bin/bowtie2 --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:10 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 691s r0 16 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU 691s (fw:1, sam:1) 691s References: 691s >0 691s ATATGCCCCATGCCCCCCTCCG 691s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 691s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:22 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 691s r0 0 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU 691s (fw:1, sam:1) 691s References: 691s >0 691s ATATGCCCCATGCCCCCCTCCG 691s /usr/bin/bowtie2 --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 691s @HD VN:1.5 SO:unsorted GO:query 691s @SQ SN:0 LN:22 691s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 691s r0 16 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU 691s Simple paired-end 13 (fw:1, sam:1) 691s References: 691s >0 691s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 691s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 692s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz 692s @HD VN:1.5 SO:unsorted GO:query 692s @SQ SN:0 LN:51 692s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" 692s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r0 129 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r1 65 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r1 129 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r2 67 0 4 255 10M = 29 35 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r2 131 0 29 255 10M = 4 -35 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r3 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r3 131 0 28 255 10M = 4 -34 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r4 65 0 5 255 10M = 31 36 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r4 129 0 31 255 10M = 5 -36 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r5 67 0 5 255 10M = 30 35 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r5 131 0 30 255 10M = 5 -35 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r6 67 0 5 255 10M = 29 34 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r6 131 0 29 255 10M = 5 -34 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r7 67 0 5 255 10M = 28 33 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r7 131 0 28 255 10M = 5 -33 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s Simple paired-end 13 (fw:0, sam:1) 692s References: 692s >0 692s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 692s /usr/bin/bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz 692s @HD VN:1.5 SO:unsorted GO:query 692s @SQ SN:0 LN:51 692s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" 692s r0 113 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r1 113 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r1 177 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r2 115 0 29 255 10M = 4 -35 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r2 179 0 4 255 10M = 29 35 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r3 115 0 28 255 10M = 4 -34 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r3 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r4 113 0 31 255 10M = 5 -36 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r4 177 0 5 255 10M = 31 36 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r5 115 0 30 255 10M = 5 -35 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r5 179 0 5 255 10M = 30 35 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r6 115 0 29 255 10M = 5 -34 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r6 179 0 5 255 10M = 29 34 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r7 115 0 28 255 10M = 5 -33 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r7 179 0 5 255 10M = 28 33 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s Simple paired-end 12 (fw:1, sam:1) 692s References: 692s >0 692s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 692s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 692s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 692s @HD VN:1.5 SO:unsorted GO:query 692s @SQ SN:0 LN:51 692s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 692s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r0 129 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r1 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r1 131 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s Simple paired-end 12 (fw:0, sam:1) 692s References: 692s >0 692s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 692s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 692s @HD VN:1.5 SO:unsorted GO:query 692s @SQ SN:0 LN:51 692s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 692s r0 113 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r1 115 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s r1 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 692s Simple paired-end 11 (fw:1, sam:1) 692s References: 692s >0 692s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 692s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 692s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 692s @HD VN:1.5 SO:unsorted GO:query 692s @SQ SN:0 LN:51 692s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 692s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r0 129 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s Simple paired-end 11 (fw:0, sam:1) 692s References: 692s >0 692s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 692s /usr/bin/bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 692s @HD VN:1.5 SO:unsorted GO:query 692s @SQ SN:0 LN:51 692s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 692s r0 113 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s Simple paired-end 10 (fw:1, sam:1) 692s References: 692s >0 692s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 692s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 692s /usr/bin/bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 692s @HD VN:1.5 SO:unsorted GO:query 692s @SQ SN:0 LN:41 692s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 692s r0 65 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s r0 129 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 692s Simple paired-end 10 (fw:0, sam:1) 692s References: 692s >0 692s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 692s /usr/bin/bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:41 693s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 693s r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 693s r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 693s Simple paired-end 9 (fw:1, sam:1) 693s References: 693s >0 693s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 693s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 693s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 693s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:81 693s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 693s r0 99 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 147 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s Simple paired-end 9 (fw:0, sam:1) 693s References: 693s >0 693s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 693s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 693s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:81 693s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 693s r0 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s Simple paired-end 8 (fw:1, sam:1) 693s References: 693s >0 693s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 693s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 693s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:81 693s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 693s r0 99 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 147 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 355 0 4 255 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 403 0 60 255 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 355 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 403 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s Simple paired-end 8 (fw:0, sam:1) 693s References: 693s >0 693s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 693s /usr/bin/bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:81 693s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 693s r0 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 339 0 60 255 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 419 0 4 255 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 339 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s r0 419 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 693s Simple paired-end 2; no --no-mixed (fw:0, sam:1) 693s References: 693s >0 693s CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC 693s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 693s /usr/bin/bowtie2 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:53 693s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 693s r0 153 0 4 255 10M = 4 0 ATATATATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UP 693s r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 693s Simple paired-end 2; --no-mixed (fw:1, sam:1) 693s References: 693s >0 693s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 693s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 693s /usr/bin/bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 693s @HD VN:1.5 SO:unsorted GO:query 693s @SQ SN:0 LN:53 693s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 693s r0 77 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 693s r0 141 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 693s Simple paired-end 2; --no-mixed (fw:0, sam:1) 693s References: 693s >0 693s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 693s /usr/bin/bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:53 694s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 694s r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 694s r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 694s Simple paired-end 1 (fw:1, sam:1) 694s References: 694s >0 694s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 694s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 694s /usr/bin/bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:53 694s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 694s r0 67 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 694s r0 131 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 694s Simple paired-end 1 (fw:0, sam:1) 694s References: 694s >0 694s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 694s /usr/bin/bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:53 694s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 694s r0 115 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 694s r0 179 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 694s (fw:1, sam:1) 694s References: 694s >0 694s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 694s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 694s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:49 694s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 694s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s (fw:0, sam:1) 694s References: 694s >0 694s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 694s /usr/bin/bowtie2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:49 694s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 694s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 694s (fw:1, sam:1) 694s References: 694s >0 694s TTGTTCGTTTGTTCGT 694s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 694s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 694s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:16 694s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 694s r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 694s (fw:0, sam:1) 694s References: 694s >0 694s TTGTTCGTTTGTTCGT 694s /usr/bin/bowtie2 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 694s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 694s @HD VN:1.5 SO:unsorted GO:query 694s @SQ SN:0 LN:16 694s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 694s r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 694s (fw:1, sam:1) 694s References: 694s >0 694s TTGTTCGT 694s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 694s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:8 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 695s (fw:0, sam:1) 695s References: 695s >0 695s TTGTTCGT 695s /usr/bin/bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:8 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 695s (fw:1, sam:1) 695s References: 695s >0 695s TTGTTCGTTTGTTCGT 695s /usr/bin/bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp 695s /usr/bin/bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:16 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 695s (fw:0, sam:1) 695s References: 695s >0 695s TTGTTCGTTTGTTCGT 695s /usr/bin/bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:16 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 695s (fw:1, sam:1) 695s References: 695s >0 695s TTGTTCGTTTGTTCGT 695s /usr/bin/bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:16 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 695s (fw:0, sam:1) 695s References: 695s >0 695s TTGTTCGTTTGTTCGT 695s /usr/bin/bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:16 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 695s (fw:1, sam:1) 695s References: 695s >0 695s TTGTTCGTTTGTTCGT 695s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:16 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 695s (fw:0, sam:1) 695s References: 695s >0 695s TTGTTCGTTTGTTCGT 695s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:16 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 695s (fw:1, sam:1) 695s References: 695s >0 695s TTGTTCGTTTGTTCGT 695s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:16 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 0 0 9 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 695s r0 256 0 1 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 695s r0 256 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU 695s r0 256 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU 695s r0 256 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU 695s r0 256 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU 695s (fw:0, sam:1) 695s References: 695s >0 695s TTGTTCGTTTGTTCGT 695s /usr/bin/bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:16 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 695s r0 16 0 1 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 695s r0 272 0 9 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 695s r0 272 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU 695s r0 272 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU 695s r0 272 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU 695s r0 272 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU 695s FASTA-continuous 1 (fw:1, sam:1) 695s References: 695s >0 695s AGCATCGATCAGTATCTGA 695s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 695s /usr/bin/bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:19 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz" 695s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 695s seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 695s FASTA-continuous 2 (fw:1, sam:1) 695s References: 695s >0 695s AGCATCGATCAGTATCTGA 695s /usr/bin/bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:19 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz" 695s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 695s seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 695s seq2_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 695s FASTA-continuous 3 (fw:1, sam:1) 695s References: 695s >0 695s AGCATCGATCAGTATCTGA 695s /usr/bin/bowtie2 --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz 695s @HD VN:1.5 SO:unsorted GO:query 695s @SQ SN:0 LN:19 695s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz" 695s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 695s FASTA-continuous 4 (fw:1, sam:1) 695s References: 695s >0 695s AGCATCGATCAGTATCTGA 696s /usr/bin/bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:19 696s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz" 696s seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 696s FASTA-continuous 5 (fw:1, sam:1) 696s References: 696s >0 696s AGCATCGATCAGTATCTGA 696s /usr/bin/bowtie2 --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:19 696s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz" 696s seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 696s FASTA-continuous 6 (fw:1, sam:1) 696s References: 696s >0 696s AGCATCGATCAG 696s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 696s /usr/bin/bowtie2 --large-index -F 10,1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:12 696s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz" 696s seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 696s seq1_1 0 0 2 255 10M * 0 0 GCATCGATCA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 696s seq1_2 0 0 3 255 10M * 0 0 CATCGATCAG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 696s Align should not fail when first seq in ref is all Ns (fw:1, sam:1) 696s References: 696s >0 696s NNNNNNNNNNNNNNN 696s >1 696s AGCATCGATCAGTATCTGA 696s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 696s Warning: Encountered reference sequence with only gaps 696s Warning: Encountered reference sequence with only gaps 696s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:15 696s @SQ SN:1 LN:19 696s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 696s 0 0 1 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 696s Align should not fail when multiple seqs are all Ns (fw:1, sam:1) 696s References: 696s >0 696s NNNNNNNNNNNNNNN 696s >1 696s NNNNNNNNNNNNNNN 696s >2 696s AGCATCGATCAGTATCTGA 696s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 696s Warning: Encountered reference sequence with only gaps 696s Warning: Encountered reference sequence with only gaps 696s Warning: Encountered reference sequence with only gaps 696s Warning: Encountered reference sequence with only gaps 696s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:15 696s @SQ SN:1 LN:15 696s @SQ SN:2 LN:19 696s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 696s 0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 696s Should account for stretch of Ns at beginning (fw:1, sam:1) 696s References: 696s >0 696s NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA 696s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 696s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG 696s @HD VN:1.5 SO:unsorted GO:query 696s @SQ SN:0 LN:34 696s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 696s 0 0 0 18 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 696s Cline 1 (fw:1, sam:1) 696s References: 696s >0 696s AGCATCGATCAGTATCTGA 696s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 697s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG 697s @HD VN:1.5 SO:unsorted GO:query 697s @SQ SN:0 LN:19 697s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 697s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 697s Cline 2 (fw:1, sam:1) 697s References: 697s >0 697s AGCATCGATCAGTATCTGA 697s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 697s @HD VN:1.5 SO:unsorted GO:query 697s @SQ SN:0 LN:19 697s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 697s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 697s Cline 2 (fw:1, sam:1) 697s References: 697s >0 697s AGCATCGATCAGTATCTGA 697s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP 697s @HD VN:1.5 SO:unsorted GO:query 697s @SQ SN:0 LN:19 697s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" 697s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG ABCDEDGHIJKLMNOP AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 697s Cline 4 (fw:1, sam:1) 697s References: 697s >0 697s AGCATCGATCAGTATCTGA 697s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO 697s Error: Read 0 has more read characters than quality values. 697s terminate called after throwing an instance of 'int' 697s Aborted (core dumped) 697s Cline 5 (fw:1, sam:1) 697s References: 697s >0 697s AGCATCGATCAGTATCTGA 697s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ 697s (ERR): bowtie2-align exited with value 134 697s Error: Read 0 has more quality values than read characters. 697s terminate called after throwing an instance of 'int' 697s Aborted (core dumped) 697s (ERR): bowtie2-align exited with value 134 697s trim-to: trim from 5'-end (fw:1, sam:1) 697s References: 697s >0 697s AGCATCGATCAGTATCTGA 697s /usr/bin/bowtie2 --large-index --trim-to 5:12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 697s 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 698s 0 0 0 7 255 12M * 0 0 GATCAGTATCTG IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 698s trim-to: trim from 3'-end (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --trim-to 3:12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 698s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 698s trim-to: trim from 3'-end (default) (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --trim-to 12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 698s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 698s trim-to: invalid position (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s 698s --trim-to: trim position must be either 3 or 5 698s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 698s Usage: 698s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 698s 698s Index filename prefix (minus trailing .X.bt2l). 698s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 698s Files with #1 mates, paired with files in . 698s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 698s Files with #2 mates, paired with files in . 698s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 698s Files with unpaired reads. 698s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 698s Files with interleaved paired-end FASTQ/FASTA reads 698s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 698s Files are unaligned BAM sorted by read name. 698s File for SAM output (default: stdout) 698s 698s , , can be comma-separated lists (no whitespace) and can be 698s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 698s 698s Options (defaults in parentheses): 698s 698s Input: 698s -q query input files are FASTQ .fq/.fastq (default) 698s --tab5 query input files are TAB5 .tab5 698s --tab6 query input files are TAB6 .tab6 698s --qseq query input files are in Illumina's qseq format 698s -f query input files are (multi-)FASTA .fa/.mfa 698s -r query input files are raw one-sequence-per-line 698s -F k:,i: query input files are continuous FASTA where reads 698s are substrings (k-mers) extracted from a FASTA file 698s and aligned at offsets 1, 1+i, 1+2i ... end of reference 698s -c , , are sequences themselves, not files 698s -s/--skip skip the first reads/pairs in the input (none) 698s -u/--upto stop after first reads/pairs (no limit) 698s -5/--trim5 trim bases from 5'/left end of reads (0) 698s -3/--trim3 trim bases from 3'/right end of reads (0) 698s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 698s If the read end is not specified then it defaults to 3 (0) 698s --phred33 qualities are Phred+33 (default) 698s --phred64 qualities are Phred+64 698s --int-quals qualities encoded as space-delimited integers 698s 698s Presets: Same as: 698s For --end-to-end: 698s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 698s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 698s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 698s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 698s 698s For --local: 698s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 698s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 698s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 698s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 698s 698s Alignment: 698s -N max # mismatches in seed alignment; can be 0 or 1 (0) 698s -L length of seed substrings; must be >3, <32 (22) 698s -i interval between seed substrings w/r/t read len (S,1,1.15) 698s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 698s --dpad include extra ref chars on sides of DP table (15) 698s --gbar disallow gaps within nucs of read extremes (4) 698s --ignore-quals treat all quality values as 30 on Phred scale (off) 698s --nofw do not align forward (original) version of read (off) 698s --norc do not align reverse-complement version of read (off) 698s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 698s scan for the optimal seeded alignments 698s --end-to-end entire read must align; no clipping (on) 698s OR 698s --local local alignment; ends might be soft clipped (off) 698s 698s Scoring: 698s --ma match bonus (0 for --end-to-end, 2 for --local) 698s --mp max penalty for mismatch; lower qual = lower penalty (6) 698s --np penalty for non-A/C/G/Ts in read/ref (1) 698s --rdg , read gap open, extend penalties (5,3) 698s --rfg , reference gap open, extend penalties (5,3) 698s --score-min min acceptable alignment score w/r/t read length 698s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 698s 698s Reporting: 698s (default) look for multiple alignments, report best, with MAPQ 698s OR 698s -k report up to alns per read; MAPQ not meaningful 698s OR 698s -a/--all report all alignments; very slow, MAPQ not meaningful 698s 698s Effort: 698s -D give up extending after failed extends in a row (15) 698s -R for reads w/ repetitive seeds, try sets of seeds (2) 698s 698s Paired-end: 698s -I/--minins minimum fragment length (0) 698s -X/--maxins maximum fragment length (500) 698s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 698s --no-mixed suppress unpaired alignments for paired reads 698s --no-discordant suppress discordant alignments for paired reads 698s --dovetail concordant when mates extend past each other 698s --no-contain not concordant when one mate alignment contains other 698s --no-overlap not concordant when mates overlap at all 698s 698s BAM: 698s --align-paired-reads 698s Bowtie2 will, by default, attempt to align unpaired BAM reads. 698s Use this option to align paired-end reads instead. 698s --preserve-tags Preserve tags from the original BAM record by 698s appending them to the end of the corresponding SAM output. 698s 698s Output: 698s -t/--time print wall-clock time taken by search phases 698s --un write unpaired reads that didn't align to 698s --al write unpaired reads that aligned at least once to 698s --un-conc write pairs that didn't align concordantly to 698s --al-conc write pairs that aligned concordantly at least once to 698s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 698s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 698s --quiet print nothing to stderr except serious errors 698s --met-file send metrics to file at (off) 698s --met-stderr send metrics to stderr (off) 698s --met report internal counters & metrics every secs (1) 698s --no-unal suppress SAM records for unaligned reads 698s --no-head suppress header lines, i.e. lines starting with @ 698s --no-sq suppress @SQ header lines 698s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 698s --rg add ("lab:value") to @RG line of SAM header. 698s Note: @RG line only printed when --rg-id is set. 698s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 698s --sam-no-qname-trunc 698s Suppress standard behavior of truncating readname at first whitespace 698s at the expense of generating non-standard SAM. 698s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 698s --soft-clipped-unmapped-tlen 698s Exclude soft-clipped bases when reporting TLEN 698s --sam-append-comment 698s Append FASTA/FASTQ comment to SAM record 698s 698s Performance: 698s -p/--threads number of alignment threads to launch (1) 698s --reorder force SAM output order to match order of input reads 698s --mm use memory-mapped I/O for index; many 'bowtie's can share 698s 698s Other: 698s --qc-filter filter out reads that are bad according to QSEQ filter 698s --seed seed for random number generator (0) 698s --non-deterministic 698s seed rand. gen. arbitrarily instead of using read attributes 698s --version print version information and quit 698s -h/--help print this usage message 698s Error: Encountered internal Bowtie 2 exception (#1) 698s Command: /usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s (ERR): bowtie2-align exited with value 1 698s trim-to: invalid count (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s 698s --trim-to: the number bases to trim must be at least 0 698s Bowtie 2 version 2.5.2 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 698s Usage: 698s bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] 698s 698s Index filename prefix (minus trailing .X.bt2l). 698s NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. 698s Files with #1 mates, paired with files in . 698s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 698s Files with #2 mates, paired with files in . 698s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 698s Files with unpaired reads. 698s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 698s Files with interleaved paired-end FASTQ/FASTA reads 698s Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). 698s Files are unaligned BAM sorted by read name. 698s File for SAM output (default: stdout) 698s 698s , , can be comma-separated lists (no whitespace) and can be 698s specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. 698s 698s Options (defaults in parentheses): 698s 698s Input: 698s -q query input files are FASTQ .fq/.fastq (default) 698s --tab5 query input files are TAB5 .tab5 698s --tab6 query input files are TAB6 .tab6 698s --qseq query input files are in Illumina's qseq format 698s -f query input files are (multi-)FASTA .fa/.mfa 698s -r query input files are raw one-sequence-per-line 698s -F k:,i: query input files are continuous FASTA where reads 698s are substrings (k-mers) extracted from a FASTA file 698s and aligned at offsets 1, 1+i, 1+2i ... end of reference 698s -c , , are sequences themselves, not files 698s -s/--skip skip the first reads/pairs in the input (none) 698s -u/--upto stop after first reads/pairs (no limit) 698s -5/--trim5 trim bases from 5'/left end of reads (0) 698s -3/--trim3 trim bases from 3'/right end of reads (0) 698s --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end 698s If the read end is not specified then it defaults to 3 (0) 698s --phred33 qualities are Phred+33 (default) 698s --phred64 qualities are Phred+64 698s --int-quals qualities encoded as space-delimited integers 698s 698s Presets: Same as: 698s For --end-to-end: 698s --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 698s --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 698s --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default) 698s --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 698s 698s For --local: 698s --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 698s --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 698s --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) 698s --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 698s 698s Alignment: 698s -N max # mismatches in seed alignment; can be 0 or 1 (0) 698s -L length of seed substrings; must be >3, <32 (22) 698s -i interval between seed substrings w/r/t read len (S,1,1.15) 698s --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) 698s --dpad include extra ref chars on sides of DP table (15) 698s --gbar disallow gaps within nucs of read extremes (4) 698s --ignore-quals treat all quality values as 30 on Phred scale (off) 698s --nofw do not align forward (original) version of read (off) 698s --norc do not align reverse-complement version of read (off) 698s --no-1mm-upfront do not allow 1 mismatch alignments before attempting to 698s scan for the optimal seeded alignments 698s --end-to-end entire read must align; no clipping (on) 698s OR 698s --local local alignment; ends might be soft clipped (off) 698s 698s Scoring: 698s --ma match bonus (0 for --end-to-end, 2 for --local) 698s --mp max penalty for mismatch; lower qual = lower penalty (6) 698s --np penalty for non-A/C/G/Ts in read/ref (1) 698s --rdg , read gap open, extend penalties (5,3) 698s --rfg , reference gap open, extend penalties (5,3) 698s --score-min min acceptable alignment score w/r/t read length 698s (G,20,8 for local, L,-0.6,-0.6 for end-to-end) 698s 698s Reporting: 698s (default) look for multiple alignments, report best, with MAPQ 698s OR 698s -k report up to alns per read; MAPQ not meaningful 698s OR 698s -a/--all report all alignments; very slow, MAPQ not meaningful 698s 698s Effort: 698s -D give up extending after failed extends in a row (15) 698s -R for reads w/ repetitive seeds, try sets of seeds (2) 698s 698s Paired-end: 698s -I/--minins minimum fragment length (0) 698s -X/--maxins maximum fragment length (500) 698s --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) 698s --no-mixed suppress unpaired alignments for paired reads 698s --no-discordant suppress discordant alignments for paired reads 698s --dovetail concordant when mates extend past each other 698s --no-contain not concordant when one mate alignment contains other 698s --no-overlap not concordant when mates overlap at all 698s 698s BAM: 698s --align-paired-reads 698s Bowtie2 will, by default, attempt to align unpaired BAM reads. 698s Use this option to align paired-end reads instead. 698s --preserve-tags Preserve tags from the original BAM record by 698s appending them to the end of the corresponding SAM output. 698s 698s Output: 698s -t/--time print wall-clock time taken by search phases 698s --un write unpaired reads that didn't align to 698s --al write unpaired reads that aligned at least once to 698s --un-conc write pairs that didn't align concordantly to 698s --al-conc write pairs that aligned concordantly at least once to 698s (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. 698s --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) 698s --quiet print nothing to stderr except serious errors 698s --met-file send metrics to file at (off) 698s --met-stderr send metrics to stderr (off) 698s --met report internal counters & metrics every secs (1) 698s --no-unal suppress SAM records for unaligned reads 698s --no-head suppress header lines, i.e. lines starting with @ 698s --no-sq suppress @SQ header lines 698s --rg-id set read group id, reflected in @RG line and RG:Z: opt field 698s --rg add ("lab:value") to @RG line of SAM header. 698s Note: @RG line only printed when --rg-id is set. 698s --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments. 698s --sam-no-qname-trunc 698s Suppress standard behavior of truncating readname at first whitespace 698s at the expense of generating non-standard SAM. 698s --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record. 698s --soft-clipped-unmapped-tlen 698s Exclude soft-clipped bases when reporting TLEN 698s --sam-append-comment 698s Append FASTA/FASTQ comment to SAM record 698s 698s Performance: 698s -p/--threads number of alignment threads to launch (1) 698s --reorder force SAM output order to match order of input reads 698s --mm use memory-mapped I/O for index; many 'bowtie's can share 698s 698s Other: 698s --qc-filter filter out reads that are bad according to QSEQ filter 698s --seed seed for random number generator (0) 698s --non-deterministic 698s seed rand. gen. arbitrarily instead of using read attributes 698s --version print version information and quit 698s -h/--help print this usage message 698s Error: Encountered internal Bowtie 2 exception (#1) 698s Command: /usr/bin/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s (ERR): bowtie2-align exited with value 1 698s Cline 7 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 698s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 698s Cline 8 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 698s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 698s Cline 9 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 698s Cline multiread 1 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 698s 698s 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 698s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 698s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 698s Cline multiread 2 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII 698s 698s 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 698s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 698s Cline multiread 3 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG 698s 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 698s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 698s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 698s Cline paired 1 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAAAAACTGA 698s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 698s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" 698s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 698s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 698s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 698s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 698s Cline paired 2 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAAAAACTGA 698s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 698s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 698s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 698s Cline paired 3 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAAAAACTGA 698s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 698s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 698s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 698s Cline paired 4 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAAAAACTGA 698s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII 698s @HD VN:1.5 SO:unsorted GO:query 698s @SQ SN:0 LN:19 698s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 698s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 698s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 698s Fastq 1 (fw:1, sam:1) 698s References: 698s >0 698s AGCATCGATCAGTATCTGA 698s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 699s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s @HD VN:1.5 SO:unsorted GO:query 699s @SQ SN:0 LN:19 699s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" 699s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 699s Fastq 2 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s @HD VN:1.5 SO:unsorted GO:query 699s @SQ SN:0 LN:19 699s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz" 699s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 699s Fastq 3 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s @HD VN:1.5 SO:unsorted GO:query 699s @SQ SN:0 LN:19 699s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz" 699s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 699s Fastq 4 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s Error: Read r0 has more read characters than quality values. 699s terminate called after throwing an instance of 'int' 699s Aborted (core dumped) 699s (ERR): bowtie2-align exited with value 134 699s Fastq 5 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s Error: Read r0 has more read characters than quality values. 699s terminate called after throwing an instance of 'int' 699s Aborted (core dumped) 699s (ERR): bowtie2-align exited with value 134 699s Fastq 6 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s Error: reads file does not look like a FASTQ file 699s terminate called after throwing an instance of 'int' 699s Aborted (core dumped) 699s (ERR): bowtie2-align exited with value 134 699s Fastq 7 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s @HD VN:1.5 SO:unsorted GO:query 699s @SQ SN:0 LN:19 699s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" 699s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 699s Fastq 8 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s @HD VN:1.5 SO:unsorted GO:query 699s @SQ SN:0 LN:19 699s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz" 699s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 699s Fastq 9 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz 699s @HD VN:1.5 SO:unsorted GO:query 699s @SQ SN:0 LN:19 699s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" 699s Fastq multiread 1 (fw:1, sam:1) 699s References: 699s >0 699s AGCATCGATCAGTATCTGA 699s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz" 700s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 700s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 700s Fastq multiread 2 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz" 700s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 700s Fastq multiread 3 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" 700s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 700s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 700s Fastq paired 1 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAAAAACTGA 700s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 700s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 700s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 700s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 700s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 700s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 700s Fastq paired 2 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAAAAACTGA 700s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 700s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 700s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 700s Fastq paired 3 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAAAAACTGA 700s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 700s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 700s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 700s Fastq paired 4 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAAAAACTGA 700s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" 700s r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 700s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 700s Fasta 1 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 700s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" 700s r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 700s Fasta 2 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" 700s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 700s Fasta 3 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz 700s @HD VN:1.5 SO:unsorted GO:query 700s @SQ SN:0 LN:19 700s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz" 700s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 700s Fasta 5 (fw:1, sam:1) 700s References: 700s >0 700s AGCATCGATCAGTATCTGA 700s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz 700s Error: reads file does not look like a FASTA file 700s terminate called after throwing an instance of 'int' 701s Aborted (core dumped) 701s (ERR): bowtie2-align exited with value 134 701s Fasta 6 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s Error: reads file does not look like a FASTA file 701s terminate called after throwing an instance of 'int' 701s Aborted (core dumped) 701s (ERR): bowtie2-align exited with value 134 701s Fasta 7 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 701s Fasta 8 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 701s Fasta 9 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s Fasta multiread 1 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 701s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 701s Fasta multiread 2 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 701s Fasta multiread 3 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 701s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 701s Fasta multiline 1 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 701s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 701s Fasta multiline 2 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 701s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 701s Fasta multiline 3 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAGTATCTGA 701s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz 701s @HD VN:1.5 SO:unsorted GO:query 701s @SQ SN:0 LN:19 701s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" 701s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 701s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 701s Fasta paired 1 (fw:1, sam:1) 701s References: 701s >0 701s AGCATCGATCAAAAACTGA 701s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 701s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 702s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 702s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 702s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 702s r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP 702s Fasta paired 2 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAAAAACTGA 702s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 702s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 702s r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP 702s Fasta paired 3 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAAAAACTGA 702s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 702s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 702s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 702s Fasta paired 4 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAAAAACTGA 702s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 702s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 702s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 702s Raw 1 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 702s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 702s Raw 2 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 702s Raw 3 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 702s Raw 7 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 702s Raw 8 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 702s Raw 9 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s Raw multiread 1 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 702s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 702s Raw multiread 2 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 702s Raw multiread 3 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAGTATCTGA 702s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz 702s @HD VN:1.5 SO:unsorted GO:query 702s @SQ SN:0 LN:19 702s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz" 702s 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 702s 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 702s Raw paired 1 (fw:1, sam:1) 702s References: 702s >0 702s AGCATCGATCAAAAACTGA 702s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 703s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 703s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 703s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 703s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 703s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 703s Raw paired 2 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAAAAACTGA 703s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 703s 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 703s 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 703s Raw paired 3 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAAAAACTGA 703s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 703s 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 703s 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 703s Raw paired 4 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAAAAACTGA 703s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 703s 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 703s 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 703s Tabbed 1 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAGTATCTGA 703s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 703s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 703s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 703s Tabbed 2 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAGTATCTGA 703s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 703s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 703s Tabbed 3 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAGTATCTGA 703s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 703s @HD VN:1.5 SO:unsorted GO:query 703s @SQ SN:0 LN:19 703s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 703s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 703s Tabbed 4 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAGTATCTGA 703s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 703s Error: Read r0 has more read characters than quality values. 703s terminate called after throwing an instance of 'int' 703s Tabbed 5 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAGTATCTGA 703s Aborted (core dumped) 703s (ERR): bowtie2-align exited with value 134 703s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 703s Error: Read r0 has more quality values than read characters. 703s terminate called after throwing an instance of 'int' 703s Aborted (core dumped) 703s (ERR): bowtie2-align exited with value 134 703s Tabbed 7 (fw:1, sam:1) 703s References: 703s >0 703s AGCATCGATCAGTATCTGA 703s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 704s Tabbed 8 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 704s Tabbed 9 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s Tabbed multiread 1 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 704s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 704s Tabbed multiread 2 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 704s Tabbed multiread 3 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 704s r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 704s Tabbed paired 1 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAAAAACTGA 704s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 704s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 704s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 704s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 704s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 704s Tabbed paired 2 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAAAAACTGA 704s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 704s r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 704s Tabbed paired 3 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAAAAACTGA 704s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 704s r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 704s Tabbed paired 4 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAAAAACTGA 704s /usr/bin/bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 704s r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 704s r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN 704s Qseq 1 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 704s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 704s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 704s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 704s Qseq 2 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 704s @HD VN:1.5 SO:unsorted GO:query 704s @SQ SN:0 LN:19 704s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 704s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 704s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 704s Qseq 3 (fw:1, sam:1) 704s References: 704s >0 704s AGCATCGATCAGTATCTGA 704s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 705s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 705s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 705s Qseq 4 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 705s Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. 705s terminate called after throwing an instance of 'int' 705s Aborted (core dumped) 705s (ERR): bowtie2-align exited with value 134 705s Qseq 7 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s /usr/bin/bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 705s MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 705s Qseq 8 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 705s /usr/bin/bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 705s MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 705s Qseq 9 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at simple_tests.pl line 5052. 705s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 705s Qseq multiread 1 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 705s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 705s MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 705s Qseq multiread 2 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s /usr/bin/bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 705s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 705s Qseq multiread 3 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAGTATCTGA 705s /usr/bin/bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" 705s MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 705s MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU 705s Qseq paired 1 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAAAAACTGA 705s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 705s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 705s MachName_RunNum_Lane_Tile_10_10_Index 99 0 1 255 10M = 9 19 AGCATCGATC ABCBGACBCB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 705s MachName_RunNum_Lane_Tile_10_10_Index 147 0 9 255 11M = 1 -19 TCAAAAACTGA ABCBCAGBCBA AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 705s MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 705s MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 705s Qseq paired 2 (fw:1, sam:1) 705s References: 705s >0 705s AGCATCGATCAAAAACTGA 705s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz 705s @HD VN:1.5 SO:unsorted GO:query 705s @SQ SN:0 LN:19 705s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" 705s MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 705s MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 705s Left-align insertion (fw:1, sam:1) 705s References: 705s >0 705s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 705s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 706s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:73 706s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 706s r0 0 0 23 24 2M1I40M * 0 0 ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:42 YT:Z:UU 706s Left-align deletion (fw:1, sam:1) 706s References: 706s >0 706s GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 706s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:73 706s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 706s r0 0 0 19 40 6M1D39M * 0 0 ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^A39 YT:Z:UU 706s Left-align insertion with mismatch at LHS (fw:1, sam:1) 706s References: 706s >0 706s GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC 706s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 706s /usr/bin/bowtie2 --large-index --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:73 706s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 706s r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU 706s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 706s References: 706s >0 706s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 706s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 706s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:1192 706s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 706s r0 65 0 3 42 38M = 1065 0 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UP 706s r0 129 0 1065 1 42M = 3 0 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UP 706s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 706s References: 706s >0 706s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG 706s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 706s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:1028 706s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 706s r0 65 0 3 42 38M = 982 1021 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:DP 706s r0 129 0 982 42 42M = 3 -1021 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:DP 706s MREVERSE flag is set if mate does not align (fw:1, sam:1) 706s References: 706s >0 706s TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG 706s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 706s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 706s @HD VN:1.5 SO:unsorted GO:query 706s @SQ SN:0 LN:250 706s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 706s r0 89 0 51 42 100M = 51 0 TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP 706s r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 706s Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) 706s References: 706s >0 706s CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG 706s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 707s /usr/bin/bowtie2 --large-index --fr --quiet --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:290 707s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 707s r0 99 0 3 1 38M = 246 285 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:CP 707s r0 147 0 246 1 42M = 3 -285 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:CP 707s MD:Z 1 (fw:1, sam:1) 707s References: 707s >0 707s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 707s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 707s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:54 707s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 707s r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU 707s MD:Z 1 (fw:0, sam:1) 707s References: 707s >0 707s CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 707s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:54 707s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 707s r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU 707s MD:Z 2 (fw:1, sam:1) 707s References: 707s >0 707s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 707s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 707s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:54 707s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 707s r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU 707s MD:Z 2 (fw:0, sam:1) 707s References: 707s >0 707s CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 707s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:54 707s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 707s r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU 707s MD:Z 3 (fw:1, sam:1) 707s References: 707s >0 707s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 707s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 707s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:55 707s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 707s r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU 707s MD:Z 3 (fw:0, sam:1) 707s References: 707s >0 707s CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 707s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 707s @HD VN:1.5 SO:unsorted GO:query 707s @SQ SN:0 LN:55 707s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 707s r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU 708s MD:Z 4 (fw:1, sam:1) 708s References: 708s >0 708s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 708s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 708s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:55 708s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 708s r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU 708s MD:Z 4 (fw:0, sam:1) 708s References: 708s >0 708s CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA 708s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:55 708s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 708s r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU 708s Local alignment 1 (fw:1, sam:1) 708s References: 708s >0 708s TTGT 708s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 708s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:4 708s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 708s r0 0 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU 708s Local alignment 1 (fw:0, sam:1) 708s References: 708s >0 708s TTGT 708s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:4 708s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 708s r0 16 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU 708s Local alignment 2 (fw:1, sam:1) 708s References: 708s >0 708s TTGA 708s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 708s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:4 708s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 708s r0 0 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 708s Local alignment 2 (fw:0, sam:1) 708s References: 708s >0 708s TTGA 708s /usr/bin/bowtie2 --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:4 708s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 708s r0 16 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 708s Local alignment 3 (fw:1, sam:1) 708s References: 708s >0 708s TTGTTCGTTTGTTCGT 708s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 708s /usr/bin/bowtie2 --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 708s @HD VN:1.5 SO:unsorted GO:query 708s @SQ SN:0 LN:16 708s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 708s r0 0 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 708s r0 256 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 709s Local alignment 3 (fw:0, sam:1) 709s References: 709s >0 709s TTGTTCGTTTGTTCGT 709s /usr/bin/bowtie2 --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:16 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 709s r0 16 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 709s r0 272 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 709s Local alignment 4 (fw:1, sam:1) 709s References: 709s >0 709s TTGTTCGTTTGTTCGT 709s /usr/bin/bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:16 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 709s r0 0 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 709s r0 256 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 709s Local alignment 4 (fw:0, sam:1) 709s References: 709s >0 709s TTGTTCGTTTGTTCGT 709s /usr/bin/bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:16 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 709s r0 16 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU 709s r0 272 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 709s Alignment order -k (fw:1, sam:1) 709s References: 709s >0 709s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 709s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 709s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:86 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 709s r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 709s r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 709s r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 709s r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 709s Alignment order -k (fw:0, sam:1) 709s References: 709s >0 709s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 709s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:86 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 709s r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 709s r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 709s r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 709s r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 709s Alignment order -a (fw:1, sam:1) 709s References: 709s >0 709s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 709s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:86 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 709s r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 709s r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 709s r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 709s r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 709s Alignment order -a (fw:0, sam:1) 709s References: 709s >0 709s GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA 709s /usr/bin/bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:86 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 709s r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 709s r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU 709s r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU 709s r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU 709s Mate reporting order, -a (fw:1, sam:1) 709s References: 709s >0 709s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 709s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 709s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:407 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 709s r0 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r2 99 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 709s r2 147 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 709s Mate reporting order, -a (fw:0, sam:1) 709s References: 709s >0 709s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 709s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:407 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 709s r0 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r2 83 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 709s r2 163 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 709s Mate reporting order, -M 1 (fw:1, sam:1) 709s References: 709s >0 709s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 709s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 709s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:407 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 709s r0 99 0 104 1 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 147 0 270 1 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 83 0 270 1 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 163 0 104 1 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r2 99 0 307 42 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 709s r2 147 0 379 42 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 709s Mate reporting order, -M 1 (fw:0, sam:1) 709s References: 709s >0 709s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA 709s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz 709s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 709s @HD VN:1.5 SO:unsorted GO:query 709s @SQ SN:0 LN:407 709s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" 709s r0 83 0 270 1 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r0 163 0 104 1 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 99 0 104 1 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r1 147 0 270 1 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 709s r2 83 0 379 42 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP 709s r2 163 0 307 42 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP 709s Non-overlapping; no args (fw:1, sam:1) 709s References: 709s >0 709s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 709s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s Non-overlapping; no args (fw:0, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-discordant (fw:1, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-discordant (fw:0, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-dovetail (fw:1, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-dovetail (fw:0, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-overlap (fw:1, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s Non-overlapping; --no-overlap (fw:0, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 710s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 710s @HD VN:1.5 SO:unsorted GO:query 710s @SQ SN:0 LN:47 710s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 710s r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP 710s r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP 710s Overlapping; no args (fw:1, sam:1) 710s References: 710s >0 710s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 710s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:47 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 711s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 711s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 711s Overlapping; no args (fw:0, sam:1) 711s References: 711s >0 711s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 711s /usr/bin/bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:47 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 711s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 711s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 711s Overlapping; --no-dovetail (fw:1, sam:1) 711s References: 711s >0 711s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 711s /usr/bin/bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:47 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 711s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 711s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 711s Overlapping; --no-dovetail (fw:0, sam:1) 711s References: 711s >0 711s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 711s /usr/bin/bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:47 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 711s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 711s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 711s Overlapping; --no-contain (fw:1, sam:1) 711s References: 711s >0 711s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 711s /usr/bin/bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:47 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 711s r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 711s r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 711s Overlapping; --no-contain (fw:0, sam:1) 711s References: 711s >0 711s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 711s /usr/bin/bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:47 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 711s r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP 711s r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP 711s Overlapping; --no-overlap (fw:1, sam:1) 711s References: 711s >0 711s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 711s /usr/bin/bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:47 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 711s r0 65 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 711s r0 129 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP 711s Overlapping; --no-overlap (fw:0, sam:1) 711s References: 711s >0 711s AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA 711s /usr/bin/bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:47 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 711s r0 113 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP 711s r0 177 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 711s Scoring params 1 (fw:1, sam:1) 711s References: 711s >0 711s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 711s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 711s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:105 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 711s r0 0 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU 711s Scoring params 1 (fw:0, sam:1) 711s References: 711s >0 711s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG 711s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:105 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 711s r0 16 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU 711s Scoring params 2 (fw:1, sam:1) 711s References: 711s >0 711s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 711s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 711s /usr/bin/bowtie2 --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 711s @HD VN:1.5 SO:unsorted GO:query 711s @SQ SN:0 LN:102 711s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 711s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 711s Scoring params 2 (fw:0, sam:1) 711s References: 711s >0 711s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 711s /usr/bin/bowtie2 --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 711s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Scoring params 3 (fw:1, sam:1) 712s References: 712s >0 712s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 712s /usr/bin/bowtie2 --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Scoring params 3 (fw:0, sam:1) 712s References: 712s >0 712s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 712s /usr/bin/bowtie2 --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Scoring params 4 (fw:1, sam:1) 712s References: 712s >0 712s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 712s /usr/bin/bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Scoring params 4 (fw:0, sam:1) 712s References: 712s >0 712s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 712s /usr/bin/bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Scoring params 5 (fw:1, sam:1) 712s References: 712s >0 712s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 712s /usr/bin/bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Scoring params 5 (fw:0, sam:1) 712s References: 712s >0 712s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 712s /usr/bin/bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Scoring params 6 (fw:1, sam:1) 712s References: 712s >0 712s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 712s /usr/bin/bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Scoring params 6 (fw:0, sam:1) 712s References: 712s >0 712s ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG 712s /usr/bin/bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:102 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU 712s Q XS:i 1a (fw:1, sam:1) 712s References: 712s >0 712s TTGTTCGATTGTTCGA 712s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 712s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:16 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 712s Q XS:i 1a (fw:0, sam:1) 712s References: 712s >0 712s TTGTTCGATTGTTCGA 712s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:16 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 712s Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) 712s References: 712s >0 712s TTGTTCGATTGTTCGA 712s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:16 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 712s Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) 712s References: 712s >0 712s TTGTTCGATTGTTCGA 712s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:16 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 712s Q XS:i 1a ! --mp 3,6 (fw:1, sam:1) 712s References: 712s >0 712s TTGTTCGATTGTTCGA 712s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:16 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 712s Q XS:i 1a ! --mp 3,6 (fw:0, sam:1) 712s References: 712s >0 712s TTGTTCGATTGTTCGA 712s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 712s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 712s @HD VN:1.5 SO:unsorted GO:query 712s @SQ SN:0 LN:16 712s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 712s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 712s Q XS:i 1a I --mp 3,3 (fw:1, sam:1) 712s References: 712s >0 712s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1a I --mp 3,3 (fw:0, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1a I --mp 3,6 (fw:1, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1a I --mp 3,6 (fw:0, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1a --ignore-quals (fw:1, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1a --ignore-quals (fw:0, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1b (fw:1, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1b (fw:0, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1b --ignore-quals (fw:1, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1b --ignore-quals (fw:0, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1c (fw:1, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1c (fw:0, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1c --ignore-quals (fw:1, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s Q XS:i 1c --ignore-quals (fw:0, sam:1) 713s References: 713s >0 713s TTGTTCGATTGTTCGA 713s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 713s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 713s @HD VN:1.5 SO:unsorted GO:query 713s @SQ SN:0 LN:16 713s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 713s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 713s (fw:1, sam:1) 713s References: 713s >0 713s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 713s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 713s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 714s @HD VN:1.5 SO:unsorted GO:query 714s @SQ SN:0 LN:68 714s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 714s r0 73 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP 714s r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 714s (fw:0, sam:1) 714s References: 714s >0 714s CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT 714s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 714s @HD VN:1.5 SO:unsorted GO:query 714s @SQ SN:0 LN:68 714s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 714s r0 137 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP 714s r0 69 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 714s (fw:1, sam:1) 714s References: 714s >0 714s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 714s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 715s /usr/bin/bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:528 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 457 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:528 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 16 0 289 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCGTTTGTTCGT 715s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 715s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCGTTTGTTCGT 715s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCGTTTGTTCGT 715s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCGTTTGTTCGT 715s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 1 (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGA 715s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 715s XS:i 1 (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGA 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU 715s XS:i 2 (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGA 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU 715s XS:i 2 (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGA 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU 715s XS:i 3a (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGT 715s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 3a (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 3b (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 3b (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 3c (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 3c (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCGATTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:16 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 4a (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCAATTGTTCGATTGTTCGT 715s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 715s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:24 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 4a (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCAATTGTTCGATTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:24 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 4b (fw:1, sam:1) 715s References: 715s >0 715s TTGTTCAATTGTTCGATTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 715s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 715s @HD VN:1.5 SO:unsorted GO:query 715s @SQ SN:0 LN:24 715s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 715s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 715s XS:i 4b (fw:0, sam:1) 715s References: 715s >0 715s TTGTTCAATTGTTCGATTGTTCGT 715s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:24 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 716s XS:i 5a (fw:1, sam:1) 716s References: 716s >0 716s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 716s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 716s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:120 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 716s XS:i 5a (fw:0, sam:1) 716s References: 716s >0 716s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 716s /usr/bin/bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:120 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 716s XS:i 5b (fw:1, sam:1) 716s References: 716s >0 716s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 716s /usr/bin/bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:120 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 716s XS:i 5b (fw:0, sam:1) 716s References: 716s >0 716s TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA 716s /usr/bin/bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:120 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 716s BWA-SW-like 1 (fw:1, sam:1) 716s References: 716s >0 716s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 716s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 716s /usr/bin/bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:64 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU 716s BWA-SW-like 1 (fw:0, sam:1) 716s References: 716s >0 716s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 716s /usr/bin/bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:64 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU 716s BWA-SW-like 2 (fw:1, sam:1) 716s References: 716s >0 716s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 716s /usr/bin/bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:64 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU 716s BWA-SW-like 2 (fw:0, sam:1) 716s References: 716s >0 716s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 716s /usr/bin/bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:64 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU 716s BWA-SW-like 3 (fw:1, sam:1) 716s References: 716s >0 716s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 716s /usr/bin/bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:64 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 0 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU 716s BWA-SW-like 3 (fw:0, sam:1) 716s References: 716s >0 716s GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA 716s /usr/bin/bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 716s @HD VN:1.5 SO:unsorted GO:query 716s @SQ SN:0 LN:64 716s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 716s r0 16 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU 716s SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) 716s References: 716s >0 716s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 716s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 717s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 99 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 717s r0 147 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 717s SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1) 717s References: 717s >0 717s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 717s /usr/bin/bowtie2 --large-index --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 67 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 717s r0 131 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 717s SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1) 717s References: 717s >0 717s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 717s /usr/bin/bowtie2 --large-index --rf --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 83 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 717s r0 163 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP 717s SAM paired-end where both mates align 1 (fw:1, sam:1) 717s References: 717s >0 717s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 717s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 99 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 717s r0 147 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 717s SAM paired-end where both mates align 2 (fw:1, sam:1) 717s References: 717s >0 717s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 717s /usr/bin/bowtie2 --large-index --rf --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 83 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 717s r0 163 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 717s SAM paired-end where both mates align 3 (fw:1, sam:1) 717s References: 717s >0 717s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 717s /usr/bin/bowtie2 --large-index --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 67 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP 717s r0 131 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP 717s SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1) 717s References: 717s >0 717s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 717s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 73 0 4 255 24M = 4 0 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YT:Z:UP 717s r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 717s SAM paired-end where neither mate aligns (fw:1, sam:1) 717s References: 717s >0 717s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 717s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 717s r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 717s SAM paired-end where both mates align, but discordantly (fw:1, sam:1) 717s References: 717s >0 717s GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC 717s /usr/bin/bowtie2 --large-index --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:69 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 717s r0 65 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YS:i:0 YT:Z:DP 717s r0 129 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP 717s matchesRef regression 4 (fw:1, sam:1) 717s References: 717s >0 717s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 717s >1 717s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 717s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 717s /usr/bin/bowtie2 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:120 717s @SQ SN:1 LN:31 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 717s r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 717s matchesRef regression 4 (fw:0, sam:1) 717s References: 717s >0 717s CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC 717s >1 717s GCTCGGAATTCGTGCTCCGNCCCGTACGGTT 717s /usr/bin/bowtie2 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 717s @HD VN:1.5 SO:unsorted GO:query 717s @SQ SN:0 LN:120 717s @SQ SN:1 LN:31 717s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 717s r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU 717s matchesRef regression 3 (fw:1, sam:1) 717s References: 717s >0 717s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 717s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 718s /usr/bin/bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:53 718s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 718s r0 16 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU 718s matchesRef regression 3 (fw:0, sam:1) 718s References: 718s >0 718s GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC 718s /usr/bin/bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:53 718s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 718s r0 0 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU 718s matchesRef regression 2 (fw:1, sam:1) 718s References: 718s >0 718s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 718s >1 718s CCTTGTTNTTAATGCTGCCTGGTTTNG 718s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 718s /usr/bin/bowtie2 --large-index --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:47 718s @SQ SN:1 LN:27 718s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 718s r0 77 * 0 0 * * 0 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 718s r0 141 * 0 0 * * 0 0 ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP 718s matchesRef regression 2 (fw:0, sam:1) 718s References: 718s >0 718s GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG 718s >1 718s CCTTGTTNTTAATGCTGCCTGGTTTNG 718s /usr/bin/bowtie2 --large-index --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:47 718s @SQ SN:1 LN:27 718s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 718s r0 83 0 1 255 29S23M = 1 -68 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:-128 YT:Z:CP 718s r0 163 0 1 255 45S15M = 1 68 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-128 XN:i:9 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:14T0 YS:i:-78 YT:Z:CP 718s matchesRef regression 1 (fw:1, sam:1) 718s References: 718s >0 718s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 718s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 718s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:61 718s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 718s r0 0 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU 718s matchesRef regression 1 (fw:0, sam:1) 718s References: 718s >0 718s AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC 718s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:61 718s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 718s r0 16 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU 718s Discordant with different chromosomes (fw:1, sam:1) 718s References: 718s >0 718s TTTATAAAAATATTTCCCCCCCC 718s >1 718s CCCCCCTGTCGCTACCGCCCCCCCCCCC 718s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 718s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 718s @HD VN:1.5 SO:unsorted GO:query 718s @SQ SN:0 LN:23 718s @SQ SN:1 LN:28 718s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 718s r0 65 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 718s r0 129 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 718s r1 65 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 718s r1 129 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 718s Discordant with different chromosomes (fw:0, sam:1) 718s References: 718s >0 718s TTTATAAAAATATTTCCCCCCCC 718s >1 718s CCCCCCTGTCGCTACCGCCCCCCCCCCC 718s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:23 719s @SQ SN:1 LN:28 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 719s r0 113 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 719s r0 177 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 719s r1 113 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 719s r1 177 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 719s (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 719s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 719s r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 719s (fw:0, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 719s r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 719s (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 719s r1 99 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 719s r1 147 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 719s (fw:0, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 719s r1 83 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 719s r1 163 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 719s (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 719s (fw:0, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 719s (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 719s (fw:0, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 719s (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 719s r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 719s (fw:0, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 719s r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU 719s (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 719s r1 0 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 719s (fw:0, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 719s r1 16 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 719s (fw:0, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 719s @HD VN:1.5 SO:unsorted GO:query 719s @SQ SN:0 LN:19 719s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 719s r1 16 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 719s (fw:1, sam:1) 719s References: 719s >0 719s AGCATCGATCAGTATCTGA 719s /usr/bin/bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:19 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 720s r1 0 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU 720s (fw:1, sam:1) 720s References: 720s >0 720s TGC 720s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 720s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:3 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 720s r0 0 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 720s (fw:0, sam:1) 720s References: 720s >0 720s TGC 720s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:3 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 720s r0 16 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU 720s (fw:1, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 720s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 720s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s (fw:0, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 720s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s (fw:1, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 720s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s (fw:0, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 720s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s (fw:1, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 720s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s (fw:0, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 720s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s (fw:1, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 720s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s (fw:0, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 720s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s (fw:1, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 720s @HD VN:1.5 SO:unsorted GO:query 720s @SQ SN:0 LN:8 720s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 720s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 720s r1 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 720s r2 0 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 720s (fw:0, sam:1) 720s References: 720s >0 720s TTGTTCGT 720s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:8 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" 721s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s r1 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 721s r2 16 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 721s (fw:1, sam:1) 721s References: 721s >0 721s TTGTTCGT 721s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:8 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 721s r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s r2 4 * 0 0 * * 0 0 GTTCGTA IIIIIII YT:Z:UU 721s r3 4 * 0 0 * * 0 0 ATTGTTC IIIIIII YT:Z:UU 721s (fw:0, sam:1) 721s References: 721s >0 721s TTGTTCGT 721s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:8 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 721s r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s r2 4 * 0 0 * * 0 0 TACGAAC IIIIIII YT:Z:UU 721s r3 4 * 0 0 * * 0 0 GAACAAT IIIIIII YT:Z:UU 721s (fw:1, sam:1) 721s References: 721s >0 721s TTGTTCGT 721s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:8 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 721s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s (fw:0, sam:1) 721s References: 721s >0 721s TTGTTCGT 721s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:8 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 721s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s (fw:1, sam:1) 721s References: 721s >0 721s TTGTTCGT 721s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:8 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 721s r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s (fw:0, sam:1) 721s References: 721s >0 721s TTGTTCGT 721s /usr/bin/bowtie2 --large-index --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:8 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 721s r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 721s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 721s References: 721s >0 721s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 721s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 721s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 721s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:1000 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 721s r0 99 0 13 1 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 147 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 721s References: 721s >0 721s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 721s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 721s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:1000 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 721s r0 83 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 163 0 13 1 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 721s References: 721s >0 721s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 721s /usr/bin/bowtie2 --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 721s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:1000 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 721s r0 99 0 13 1 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 721s r0 147 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 721s P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 721s References: 721s >0 721s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 721s /usr/bin/bowtie2 --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 721s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:1000 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 721s r0 83 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 721s r0 163 0 13 1 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 721s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) 721s References: 721s >0 721s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 721s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:1000 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 721s r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 355 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 403 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 355 0 13 255 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 403 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 355 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 403 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 355 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 403 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) 721s References: 721s >0 721s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 721s /usr/bin/bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:1000 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 721s r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 339 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 419 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 339 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 419 0 13 255 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 339 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 419 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 721s r0 419 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 721s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) 721s References: 721s >0 721s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 721s /usr/bin/bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 721s @HD VN:1.5 SO:unsorted GO:query 721s @SQ SN:0 LN:1000 721s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 721s r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 721s r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 721s r0 355 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 721s r0 403 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 721s r0 355 0 13 255 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 721s r0 403 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 721s r0 355 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 721s r0 403 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 721s r0 355 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 721s r0 403 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 721s P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1) 721s References: 721s >0 721s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT 721s /usr/bin/bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:1000 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s r0 339 0 961 255 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s r0 419 0 13 255 33M = 961 976 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s r0 339 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s r0 419 0 13 255 33M = 553 568 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s r0 339 0 487 255 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s r0 419 0 13 255 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s r0 419 0 13 255 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 722s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 722s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 722s P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 722s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 722s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 99 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 722s r0 147 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 722s P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 83 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 722s r0 163 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 722s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 99 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s r0 147 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 83 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s r0 163 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 722s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 722s P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 722s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 722s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2 --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 722s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 722s @HD VN:1.5 SO:unsorted GO:query 722s @SQ SN:0 LN:363 722s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 722s r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 722s r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 722s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 722s References: 722s >0 722s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 722s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 723s /usr/bin/bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:126 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 723s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 723s P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 723s /usr/bin/bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:126 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 723s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 723s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 723s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:126 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 723s r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 723s P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 723s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:126 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 723s r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 723s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 723s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:126 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 99 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 723s r0 147 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 723s P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 723s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:126 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 83 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 723s r0 163 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 723s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 723s /usr/bin/bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:126 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 99 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 723s r0 147 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 723s P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA 723s /usr/bin/bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:126 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 83 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 723s r0 163 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 723s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 723s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 723s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:2607 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 99 0 1909 1 33M = 1975 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 723s r0 147 0 1975 1 28M = 1909 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 723s P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA 723s /usr/bin/bowtie2 --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 723s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 723s @HD VN:1.5 SO:unsorted GO:query 723s @SQ SN:0 LN:2607 723s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 723s r0 83 0 1975 1 28M = 1909 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP 723s r0 163 0 1909 1 33M = 1975 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP 723s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1) 723s References: 723s >0 723s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 723s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 724s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 724s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:1906 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 724s r0 99 0 1672 1 33M = 1738 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 724s r0 147 0 1738 1 28M = 1672 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 724s P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC 724s /usr/bin/bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 724s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:1906 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 724s r0 83 0 1738 1 28M = 1672 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP 724s r0 163 0 1672 1 33M = 1738 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP 724s U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 724s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 724s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:56 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 0 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 724s U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 724s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:56 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 16 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 724s U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 724s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:56 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 0 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 724s U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 724s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:56 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 16 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 724s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 724s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:56 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 724s U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 724s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:56 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 724s U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 724s /usr/bin/bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:56 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 724s U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1) 724s References: 724s >0 724s AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA 724s /usr/bin/bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:56 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU 724s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) 724s References: 724s >0 724s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 724s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 724s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 724s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 724s @HD VN:1.5 SO:unsorted GO:query 724s @SQ SN:0 LN:85 724s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 724s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 724s U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) 724s References: 724s >0 724s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 724s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --quiet -k 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 725s @HD VN:1.5 SO:unsorted GO:query 725s @SQ SN:0 LN:85 725s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 725s r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 725s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 725s References: 725s >0 725s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 725s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 726s /usr/bin/bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:340 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 726s References: 726s >0 726s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 726s /usr/bin/bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:340 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) 726s References: 726s >0 726s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 726s /usr/bin/bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:340 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) 726s References: 726s >0 726s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 726s /usr/bin/bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:340 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) 726s References: 726s >0 726s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 726s /usr/bin/bowtie2 --large-index --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:340 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 0 0 219 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 256 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1) 726s References: 726s >0 726s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 726s /usr/bin/bowtie2 --large-index --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:340 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 16 0 262 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 272 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 272 0 304 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 272 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1) 726s References: 726s >0 726s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 726s /usr/bin/bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:340 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 0 0 219 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 256 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1) 726s References: 726s >0 726s AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA 726s /usr/bin/bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:340 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 16 0 262 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 272 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 272 0 304 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s r0 272 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 726s (fw:1, sam:1) 726s References: 726s >0 726s TTGTTCGTTTGTTCGT 726s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 726s /usr/bin/bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:16 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 0 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 726s r0 256 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 726s (fw:0, sam:1) 726s References: 726s >0 726s TTGTTCGTTTGTTCGT 726s /usr/bin/bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:16 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 16 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 726s r0 272 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU 726s (fw:1, sam:1) 726s References: 726s >0 726s TTGTTCGTTTGTTCGT 726s /usr/bin/bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:16 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 4 * 0 0 * * 0 0 TTGTTCAT IIIIIIII YT:Z:UU 726s (fw:0, sam:1) 726s References: 726s >0 726s TTGTTCGTTTGTTCGT 726s /usr/bin/bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 726s @HD VN:1.5 SO:unsorted GO:query 726s @SQ SN:0 LN:16 726s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 726s r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU 726s (fw:1, sam:1) 726s References: 726s >0 726s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 726s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 727s /usr/bin/bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:49 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 727s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s (fw:0, sam:1) 727s References: 727s >0 727s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 727s /usr/bin/bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:49 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 727s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 727s Gap penalties 1 (fw:1, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 0 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU 727s Gap penalties 1 (fw:0, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 16 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU 727s Gap penalties 2 (fw:1, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 4 * 0 0 * * 0 0 TTGTTCTTTGTT IIIIIIIIIIII YT:Z:UU 727s Gap penalties 2 (fw:0, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 4 * 0 0 * * 0 0 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU 727s Gap penalties 3 (fw:1, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 727s Gap penalties 3 (fw:0, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 727s Gap penalties 4 (fw:1, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 727s Gap penalties 4 (fw:0, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 727s Gap penalties 5 (fw:1, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU 727s Gap penalties 5 (fw:0, sam:1) 727s References: 727s >0 727s TTGTTCGTTTGTTCGT 727s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 727s @HD VN:1.5 SO:unsorted GO:query 727s @SQ SN:0 LN:16 727s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 727s r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU 727s Gap penalties 6 (fw:1, sam:1) 727s References: 727s >0 727s ATTGTTCGTTTGTTCGTA 727s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 728s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:18 728s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 728s r0 0 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU 728s Gap penalties 6 (fw:0, sam:1) 728s References: 728s >0 728s ATTGTTCGTTTGTTCGTA 728s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:18 728s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 728s r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU 728s Gap penalties 7 (fw:1, sam:1) 728s References: 728s >0 728s TTGTTCGTTTGTTCGT 728s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 728s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:16 728s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 728s r0 4 * 0 0 * * 0 0 TTGTTGTTTGATTCGT IIIIIIIIIIIIIIII YT:Z:UU 728s Gap penalties 7 (fw:0, sam:1) 728s References: 728s >0 728s TTGTTCGTTTGTTCGT 728s /usr/bin/bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:16 728s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 728s r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU 728s N filtering 1 (fw:1, sam:1) 728s References: 728s >0 728s GAGACTTTATACGCATCGAACTATCGCTCTA 728s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 728s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:31 728s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 728s r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 728s N filtering 1 (fw:0, sam:1) 728s References: 728s >0 728s GAGACTTTATACGCATCGAACTATCGCTCTA 728s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:31 728s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 728s r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU 728s N filtering 2 (fw:1, sam:1) 728s References: 728s >0 728s GAGACTTTATNCGCATCGAACTATCGCTCTA 728s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 728s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 728s @HD VN:1.5 SO:unsorted GO:query 728s @SQ SN:0 LN:31 728s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 728s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 728s N filtering 2 (fw:0, sam:1) 728s References: 728s >0 728s GAGACTTTATNCGCATCGAACTATCGCTCTA 728s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 729s @HD VN:1.5 SO:unsorted GO:query 729s @SQ SN:0 LN:31 729s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 729s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 729s N filtering 3 (fw:1, sam:1) 729s References: 729s >0 729s GAGACTTTATACGCATCGAANTATCGCTCTA 729s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 729s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 729s @HD VN:1.5 SO:unsorted GO:query 729s @SQ SN:0 LN:31 729s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 729s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 729s N filtering 3 (fw:0, sam:1) 729s References: 729s >0 729s GAGACTTTATACGCATCGAANTATCGCTCTA 729s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 729s @HD VN:1.5 SO:unsorted GO:query 729s @SQ SN:0 LN:31 729s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 729s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 729s N filtering 4 (fw:1, sam:1) 729s References: 729s >0 729s GAGACTTTNTACGCATCGAACTATCGCTCTA 729s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 729s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 729s @HD VN:1.5 SO:unsorted GO:query 729s @SQ SN:0 LN:31 729s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 729s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 729s N filtering 4 (fw:0, sam:1) 729s References: 729s >0 729s GAGACTTTNTACGCATCGAACTATCGCTCTA 729s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 729s @HD VN:1.5 SO:unsorted GO:query 729s @SQ SN:0 LN:31 729s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 729s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 729s N filtering 5 (fw:1, sam:1) 729s References: 729s >0 729s GAGACTTTATNCGCATCGAACTATCGCTCTA 729s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 729s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 729s @HD VN:1.5 SO:unsorted GO:query 729s @SQ SN:0 LN:31 729s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 729s r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU 729s N filtering 5 (fw:0, sam:1) 729s References: 729s >0 729s GAGACTTTATNCGCATCGAACTATCGCTCTA 729s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 729s @HD VN:1.5 SO:unsorted GO:query 729s @SQ SN:0 LN:31 729s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 729s r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU 729s N filtering 6 (fw:1, sam:1) 729s References: 729s >0 729s GAGACTTTNTACGCATCGAANTATCGCTCTA 729s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 730s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:31 730s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 730s r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU 730s N filtering 6 (fw:0, sam:1) 730s References: 730s >0 730s GAGACTTTNTACGCATCGAANTATCGCTCTA 730s /usr/bin/bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:31 730s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 730s r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU 730s (fw:1, sam:1) 730s References: 730s >0 730s TTTTGTTCGTTTG 730s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 730s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:13 730s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 730s r0 0 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 730s (fw:0, sam:1) 730s References: 730s >0 730s TTTTGTTCGTTTG 730s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:13 730s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 730s r0 16 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 730s (fw:1, sam:1) 730s References: 730s >0 730s TTGTTCGTTTGTT 730s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 730s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:13 730s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 730s r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 730s (fw:0, sam:1) 730s References: 730s >0 730s TTGTTCGTTTGTT 730s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:13 730s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 730s r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 730s (fw:1, sam:1) 730s References: 730s >0 730s ACNCA 730s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 730s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:5 730s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 730s r0 0 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 730s (fw:0, sam:1) 730s References: 730s >0 730s ACNCA 730s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 730s @HD VN:1.5 SO:unsorted GO:query 730s @SQ SN:0 LN:5 730s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 730s r0 16 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 730s N ceil = 0, 2 legit hits (1) (fw:1, sam:1) 730s References: 730s >0 730s ACNCA 730s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:5 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 731s r0 0 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s N ceil = 0, 2 legit hits (1) (fw:0, sam:1) 731s References: 731s >0 731s ACNCA 731s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:5 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 731s r0 16 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s N ceil = 0, 2 legit hits (2) (fw:1, sam:1) 731s References: 731s >0 731s ACNCANNNNNNNNCGNNNNNNNNCG 731s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 731s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:25 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 731s r0 16 0 24 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s N ceil = 0, 2 legit hits (2) (fw:0, sam:1) 731s References: 731s >0 731s ACNCANNNNNNNNCGNNNNNNNNCG 731s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:25 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 731s r0 16 0 24 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s (fw:1, sam:1) 731s References: 731s >0 731s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 731s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 731s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:37 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 731s r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s (fw:0, sam:1) 731s References: 731s >0 731s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 731s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:37 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 731s r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s (fw:1, sam:1) 731s References: 731s >0 731s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 731s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:37 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 731s r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s (fw:0, sam:1) 731s References: 731s >0 731s ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN 731s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:37 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 731s r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 731s (fw:1, sam:1) 731s References: 731s >0 731s TTGTTYGT 731s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 731s /usr/bin/bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz 731s @HD VN:1.5 SO:unsorted GO:query 731s @SQ SN:0 LN:8 731s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" 731s r0 0 0 1 255 8M * 0 0 TTGTTGGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU 731s r1 0 0 1 255 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU 731s (fw:1, sam:1) 731s References: 731s >0 731s ATAACCTTCG 731s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 732s /usr/bin/bowtie2 --large-index --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 732s @HD VN:1.5 SO:unsorted GO:query 732s @SQ SN:0 LN:10 732s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 732s r0 0 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU 732s (fw:0, sam:1) 732s References: 732s >0 732s ATAACCTTCG 732s /usr/bin/bowtie2 --large-index --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 732s @HD VN:1.5 SO:unsorted GO:query 732s @SQ SN:0 LN:10 732s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 732s r0 16 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU 732s (fw:1, sam:1) 732s References: 732s >0 732s ATATGCCCCATGCCCCCCTCCG 732s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 732s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 732s @HD VN:1.5 SO:unsorted GO:query 732s @SQ SN:0 LN:22 732s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 732s r0 0 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU 732s (fw:1, sam:1) 732s References: 732s >0 732s ATATGCCCCATGCCCCCCTCCG 732s /usr/bin/bowtie2 --large-index --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 732s @HD VN:1.5 SO:unsorted GO:query 732s @SQ SN:0 LN:22 732s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 732s r0 16 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU 732s Simple paired-end 13 (fw:1, sam:1) 732s References: 732s >0 732s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 732s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 732s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz 732s @HD VN:1.5 SO:unsorted GO:query 732s @SQ SN:0 LN:51 732s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" 732s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r0 129 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r1 65 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r1 129 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r2 67 0 4 255 10M = 29 35 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r2 131 0 29 255 10M = 4 -35 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r3 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r3 131 0 28 255 10M = 4 -34 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r4 65 0 5 255 10M = 31 36 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r4 129 0 31 255 10M = 5 -36 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r5 67 0 5 255 10M = 30 35 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r5 131 0 30 255 10M = 5 -35 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r6 67 0 5 255 10M = 29 34 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r6 131 0 29 255 10M = 5 -34 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r7 67 0 5 255 10M = 28 33 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r7 131 0 28 255 10M = 5 -33 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s Simple paired-end 13 (fw:0, sam:1) 732s References: 732s >0 732s TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC 732s /usr/bin/bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz 732s @HD VN:1.5 SO:unsorted GO:query 732s @SQ SN:0 LN:51 732s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" 732s r0 113 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r1 113 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r1 177 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r2 115 0 29 255 10M = 4 -35 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r2 179 0 4 255 10M = 29 35 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r3 115 0 28 255 10M = 4 -34 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r3 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r4 113 0 31 255 10M = 5 -36 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r4 177 0 5 255 10M = 31 36 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 732s r5 115 0 30 255 10M = 5 -35 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r5 179 0 5 255 10M = 30 35 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r6 115 0 29 255 10M = 5 -34 CTGTCGCTAC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r6 179 0 5 255 10M = 29 34 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r7 115 0 28 255 10M = 5 -33 CCTGTCGCTA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s r7 179 0 5 255 10M = 28 33 TAAAAATATT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 732s Simple paired-end 12 (fw:1, sam:1) 732s References: 732s >0 732s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 732s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 732s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:51 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 733s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s r0 129 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s r1 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 733s r1 131 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 733s Simple paired-end 12 (fw:0, sam:1) 733s References: 733s >0 733s TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC 733s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:51 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 733s r0 113 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s r1 115 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 733s r1 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 733s Simple paired-end 11 (fw:1, sam:1) 733s References: 733s >0 733s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 733s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 733s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:51 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 733s r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s r0 129 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s Simple paired-end 11 (fw:0, sam:1) 733s References: 733s >0 733s TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC 733s /usr/bin/bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:51 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 733s r0 113 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s Simple paired-end 10 (fw:1, sam:1) 733s References: 733s >0 733s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 733s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 733s /usr/bin/bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:41 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 733s r0 65 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s r0 129 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s Simple paired-end 10 (fw:0, sam:1) 733s References: 733s >0 733s TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC 733s /usr/bin/bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:41 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 733s r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP 733s Simple paired-end 9 (fw:1, sam:1) 733s References: 733s >0 733s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 733s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 733s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 733s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:81 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 733s r0 99 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 733s r0 147 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 733s Simple paired-end 9 (fw:0, sam:1) 733s References: 733s >0 733s CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC 733s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 733s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 733s @HD VN:1.5 SO:unsorted GO:query 733s @SQ SN:0 LN:81 733s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 733s r0 83 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 733s r0 163 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 733s Simple paired-end 8 (fw:1, sam:1) 733s References: 733s >0 733s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 733s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 734s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 734s @HD VN:1.5 SO:unsorted GO:query 734s @SQ SN:0 LN:81 734s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 734s r0 99 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 147 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 355 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 403 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 355 0 20 255 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 403 0 60 255 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s Simple paired-end 8 (fw:0, sam:1) 734s References: 734s >0 734s CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC 734s /usr/bin/bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 734s @HD VN:1.5 SO:unsorted GO:query 734s @SQ SN:0 LN:81 734s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 734s r0 83 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 163 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 339 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 419 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 339 0 60 255 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 419 0 20 255 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s Simple paired-end 2; no --no-mixed (fw:0, sam:1) 734s References: 734s >0 734s CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC 734s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 734s /usr/bin/bowtie2 --large-index -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 734s @HD VN:1.5 SO:unsorted GO:query 734s @SQ SN:0 LN:53 734s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 734s r0 153 0 4 255 10M = 4 0 ATATATATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UP 734s r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 734s Simple paired-end 2; --no-mixed (fw:1, sam:1) 734s References: 734s >0 734s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 734s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 734s /usr/bin/bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 734s @HD VN:1.5 SO:unsorted GO:query 734s @SQ SN:0 LN:53 734s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 734s r0 77 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 734s r0 141 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 734s Simple paired-end 2; --no-mixed (fw:0, sam:1) 734s References: 734s >0 734s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC 734s /usr/bin/bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 734s @HD VN:1.5 SO:unsorted GO:query 734s @SQ SN:0 LN:53 734s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 734s r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP 734s r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP 734s Simple paired-end 1 (fw:1, sam:1) 734s References: 734s >0 734s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 734s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 734s /usr/bin/bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 734s @HD VN:1.5 SO:unsorted GO:query 734s @SQ SN:0 LN:53 734s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 734s r0 67 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 131 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s Simple paired-end 1 (fw:0, sam:1) 734s References: 734s >0 734s CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC 734s /usr/bin/bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz 734s @HD VN:1.5 SO:unsorted GO:query 734s @SQ SN:0 LN:53 734s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" 734s r0 115 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s r0 179 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 734s (fw:1, sam:1) 734s References: 734s >0 734s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 734s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 735s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 735s @HD VN:1.5 SO:unsorted GO:query 735s @SQ SN:0 LN:49 735s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 735s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s (fw:0, sam:1) 735s References: 735s >0 735s AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC 735s /usr/bin/bowtie2 --large-index --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz 735s @HD VN:1.5 SO:unsorted GO:query 735s @SQ SN:0 LN:49 735s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" 735s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU 735s (fw:1, sam:1) 735s References: 735s >0 735s TTGTTCGTTTGTTCGT 735s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 735s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 735s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 735s @HD VN:1.5 SO:unsorted GO:query 735s @SQ SN:0 LN:16 735s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 735s r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 735s (fw:0, sam:1) 735s References: 735s >0 735s TTGTTCGTTTGTTCGT 735s /usr/bin/bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 735s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 735s @HD VN:1.5 SO:unsorted GO:query 735s @SQ SN:0 LN:16 735s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 735s r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 735s (fw:1, sam:1) 735s References: 735s >0 735s TTGTTCGT 735s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 735s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 735s @HD VN:1.5 SO:unsorted GO:query 735s @SQ SN:0 LN:8 735s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 735s r0 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 735s (fw:0, sam:1) 735s References: 735s >0 735s TTGTTCGT 735s /usr/bin/bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 735s @HD VN:1.5 SO:unsorted GO:query 735s @SQ SN:0 LN:8 735s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 735s r0 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU 735s (fw:1, sam:1) 735s References: 735s >0 735s TTGTTCGTTTGTTCGT 735s /usr/bin/bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp 735s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 735s @HD VN:1.5 SO:unsorted GO:query 735s @SQ SN:0 LN:16 735s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 735s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 735s (fw:0, sam:1) 735s References: 735s >0 735s TTGTTCGTTTGTTCGT 735s /usr/bin/bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:16 736s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 736s (fw:1, sam:1) 736s References: 736s >0 736s TTGTTCGTTTGTTCGT 736s /usr/bin/bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:16 736s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 736s (fw:0, sam:1) 736s References: 736s >0 736s TTGTTCGTTTGTTCGT 736s /usr/bin/bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:16 736s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 736s (fw:1, sam:1) 736s References: 736s >0 736s TTGTTCGTTTGTTCGT 736s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:16 736s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU 736s (fw:0, sam:1) 736s References: 736s >0 736s TTGTTCGTTTGTTCGT 736s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:16 736s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU 736s (fw:1, sam:1) 736s References: 736s >0 736s TTGTTCGTTTGTTCGT 736s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:16 736s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s r0 0 0 9 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 736s r0 256 0 1 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 736s r0 256 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU 736s r0 256 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU 736s r0 256 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU 736s r0 256 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU 736s (fw:0, sam:1) 736s References: 736s >0 736s TTGTTCGTTTGTTCGT 736s /usr/bin/bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz 736s @HD VN:1.5 SO:unsorted GO:query 736s @SQ SN:0 LN:16 736s @PG ID:bowtie2 PN:bowtie2 VN:2.5.2 CL:"/usr/bin/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 736s r0 16 0 1 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 736s r0 272 0 9 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU 736s r0 272 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU 736s r0 272 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU 736s r0 272 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU 736s r0 272 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU 736s PASSED 736s Created DNA generator 736s N frac: 0.026 736s IUPAC frac: 0.009 736s AT/ACGT frac: 0.547 736s A/AT frac: 0.610 736s C/CG frac: 0.700 736s Generating 2 references 736s Generated reference 'Sim.pm.1' of untrimmed length 71, trimmed length 33 736s Generated reference 'Sim.pm.2' of untrimmed length 115, trimmed length 61 736s Wrote references to /tmp/Sim.pm.WCUbbuUs.fa 736s A: 27 736s C: 24 736s G: 16 736s N: 8 736s T: 19 736s Executing: /usr/bin/bowtie2-build --offrate 2 --threads 2 --dcv 16 /tmp/Sim.pm.WCUbbuUs.fa /tmp/Sim.pm.WCUbbuUs 736s *** TEST CASE *** 736s Settings: 736s Output files: "/tmp/Sim.pm.WCUbbuUs.*.bt2" 736s Building a SMALL index 736s Line rate: 6 (line is 64 bytes) 736s Lines per side: 1 (side is 64 bytes) 736s Offset rate: 2 (one in 4) 736s FTable chars: 10 736s Strings: unpacked 736s Max bucket size: default 736s Max bucket size, sqrt multiplier: default 736s Max bucket size, len divisor: 8 736s Difference-cover sample period: 16 736s Endianness: little 736s Actual local endianness: little 736s Sanity checking: disabled 736s Assertions: disabled 736s Random seed: 0 736s Sizeofs: void*:8, int:4, long:8, size_t:8 736s Input files DNA, FASTA: 736s /tmp/Sim.pm.WCUbbuUs.fa 736s Reading reference sizes 736s Time reading reference sizes: 00:00:00 736s Calculating joined length 736s Writing header 736s Reserving space for joined string 736s Joining reference sequences 736s Time to join reference sequences: 00:00:00 736s bmax according to bmaxDivN setting: 10 736s Using parameters --bmax 8 --dcv 16 736s Doing ahead-of-time memory usage test 736s Passed! Constructing with these parameters: --bmax 8 --dcv 16 736s Constructing suffix-array element generator 736s Building DifferenceCoverSample 736s Building sPrime 736s Building sPrimeOrder 736s V-Sorting samples 736s V-Sorting samples time: 00:00:00 736s Allocating rank array 736s Ranking v-sort output 736s Ranking v-sort output time: 00:00:00 736s Invoking Larsson-Sadakane on ranks 736s Invoking Larsson-Sadakane on ranks time: 00:00:00 736s Sanity-checking and returning 736s Building samples 736s Reserving space for 26 sample suffixes 736s Generating random suffixes 736s QSorting 26 sample offsets, eliminating duplicates 736s QSorting sample offsets, eliminating duplicates time: 00:00:00 736s Multikey QSorting 24 samples 736s (Using difference cover) 736s Multikey QSorting samples time: 00:00:00 736s Calculating bucket sizes 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Split 3, merged 13; iterating... 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Split 2, merged 2; iterating... 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Avg bucket size: 4.8 (target: 7) 736s Converting suffix-array elements to index image 736s Allocating ftab, absorbFtab 736s Entering Ebwt loop 736s Getting block 1 of 15 736s Reserving size (8) for bucket 1 736s Calculating Z arrays for bucket 1 736s Entering block accumulator loop for bucket 1: 736s bucket 1: 10% 736s bucket 1: 20% 736s bucket 1: 30% 736s bucket 1: 40% 736s bucket 1: 50% 736s bucket 1: 60% 736s bucket 1: 70% 736s bucket 1: 80% 736s bucket 1: 90% 736s bucket 1: 100% 736s Sorting block of length 6 for bucket 1 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 7 for bucket 1 736s Getting block 2 of 15 736s Reserving size (8) for bucket 2 736s Calculating Z arrays for bucket 2 736s Entering block accumulator loop for bucket 2: 736s bucket 2: 10% 736s bucket 2: 20% 736s bucket 2: 30% 736s bucket 2: 40% 736s bucket 2: 50% 736s bucket 2: 60% 736s bucket 2: 70% 736s bucket 2: 80% 736s bucket 2: 90% 736s bucket 2: 100% 736s Sorting block of length 7 for bucket 2 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 8 for bucket 2 736s Getting block 3 of 15 736s Reserving size (8) for bucket 3 736s Calculating Z arrays for bucket 3 736s Entering block accumulator loop for bucket 3: 736s bucket 3: 10% 736s bucket 3: 20% 736s bucket 3: 30% 736s bucket 3: 40% 736s bucket 3: 50% 736s bucket 3: 60% 736s bucket 3: 70% 736s bucket 3: 80% 736s bucket 3: 90% 736s bucket 3: 100% 736s Sorting block of length 5 for bucket 3 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 6 for bucket 3 736s Getting block 4 of 15 736s Reserving size (8) for bucket 4 736s Calculating Z arrays for bucket 4 736s Entering block accumulator loop for bucket 4: 736s bucket 4: 10% 736s bucket 4: 20% 736s bucket 4: 30% 736s bucket 4: 40% 736s bucket 4: 50% 736s bucket 4: 60% 736s bucket 4: 70% 736s bucket 4: 80% 736s bucket 4: 90% 736s bucket 4: 100% 736s Sorting block of length 3 for bucket 4 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 4 for bucket 4 736s Getting block 5 of 15 736s Reserving size (8) for bucket 5 736s Calculating Z arrays for bucket 5 736s Entering block accumulator loop for bucket 5: 736s bucket 5: 10% 736s bucket 5: 20% 736s bucket 5: 30% 736s bucket 5: 40% 736s bucket 5: 50% 736s bucket 5: 60% 736s bucket 5: 70% 736s bucket 5: 80% 736s bucket 5: 90% 736s bucket 5: 100% 736s Sorting block of length 5 for bucket 5 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 6 for bucket 5 736s Getting block 6 of 15 736s Reserving size (8) for bucket 6 736s Calculating Z arrays for bucket 6 736s Entering block accumulator loop for bucket 6: 736s bucket 6: 10% 736s bucket 6: 20% 736s bucket 6: 30% 736s bucket 6: 40% 736s bucket 6: 50% 736s bucket 6: 60% 736s bucket 6: 70% 736s bucket 6: 80% 736s bucket 6: 90% 736s bucket 6: 100% 736s Sorting block of length 6 for bucket 6 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 7 for bucket 6 736s Getting block 7 of 15 736s Reserving size (8) for bucket 7 736s Calculating Z arrays for bucket 7 736s Entering block accumulator loop for bucket 7: 736s bucket 7: 10% 736s bucket 7: 20% 736s bucket 7: 30% 736s bucket 7: 40% 736s bucket 7: 50% 736s bucket 7: 60% 736s bucket 7: 70% 736s bucket 7: 80% 736s bucket 7: 90% 736s bucket 7: 100% 736s Sorting block of length 4 for bucket 7 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 5 for bucket 7 736s Getting block 8 of 15 736s Reserving size (8) for bucket 8 736s Calculating Z arrays for bucket 8 736s Entering block accumulator loop for bucket 8: 736s bucket 8: 10% 736s bucket 8: 20% 736s bucket 8: 30% 736s bucket 8: 40% 736s bucket 8: 50% 736s bucket 8: 60% 736s bucket 8: 70% 736s bucket 8: 80% 736s bucket 8: 90% 736s bucket 8: 100% 736s Sorting block of length 3 for bucket 8 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 4 for bucket 8 736s Getting block 9 of 15 736s Reserving size (8) for bucket 9 736s Calculating Z arrays for bucket 9 736s Entering block accumulator loop for bucket 9: 736s bucket 9: 10% 736s bucket 9: 20% 736s bucket 9: 30% 736s bucket 9: 40% 736s bucket 9: 50% 736s bucket 9: 60% 736s bucket 9: 70% 736s bucket 9: 80% 736s bucket 9: 90% 736s bucket 9: 100% 736s Sorting block of length 6 for bucket 9 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 7 for bucket 9 736s Getting block 10 of 15 736s Reserving size (8) for bucket 10 736s Calculating Z arrays for bucket 10 736s Entering block accumulator loop for bucket 10: 736s bucket 10: 10% 736s bucket 10: 20% 736s bucket 10: 30% 736s bucket 10: 40% 736s bucket 10: 50% 736s bucket 10: 60% 736s bucket 10: 70% 736s bucket 10: 80% 736s bucket 10: 90% 736s bucket 10: 100% 736s Sorting block of length 1 for bucket 10 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 2 for bucket 10 736s Getting block 11 of 15 736s Reserving size (8) for bucket 11 736s Calculating Z arrays for bucket 11 736s Entering block accumulator loop for bucket 11: 736s bucket 11: 10% 736s bucket 11: 20% 736s bucket 11: 30% 736s bucket 11: 40% 736s bucket 11: 50% 736s bucket 11: 60% 736s bucket 11: 70% 736s bucket 11: 80% 736s bucket 11: 90% 736s bucket 11: 100% 736s Sorting block of length 7 for bucket 11 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 8 for bucket 11 736s Getting block 12 of 15 736s Reserving size (8) for bucket 12 736s Calculating Z arrays for bucket 12 736s Entering block accumulator loop for bucket 12: 736s bucket 12: 10% 736s bucket 12: 20% 736s bucket 12: 30% 736s bucket 12: 40% 736s bucket 12: 50% 736s bucket 12: 60% 736s bucket 12: 70% 736s bucket 12: 80% 736s bucket 12: 90% 736s bucket 12: 100% 736s Sorting block of length 7 for bucket 12 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 8 for bucket 12 736s Getting block 13 of 15 736s Reserving size (8) for bucket 13 736s Calculating Z arrays for bucket 13 736s Entering block accumulator loop for bucket 13: 736s bucket 13: 10% 736s bucket 13: 20% 736s bucket 13: 30% 736s bucket 13: 40% 736s bucket 13: 50% 736s bucket 13: 60% 736s bucket 13: 70% 736s bucket 13: 80% 736s bucket 13: 90% 736s bucket 13: 100% 736s Sorting block of length 5 for bucket 13 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 6 for bucket 13 736s Getting block 14 of 15 736s Reserving size (8) for bucket 14 736s Calculating Z arrays for bucket 14 736s Entering block accumulator loop for bucket 14: 736s bucket 14: 10% 736s bucket 14: 20% 736s bucket 14: 30% 736s bucket 14: 40% 736s bucket 14: 50% 736s bucket 14: 60% 736s bucket 14: 70% 736s bucket 14: 80% 736s bucket 14: 90% 736s bucket 14: 100% 736s Sorting block of length 2 for bucket 14 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 3 for bucket 14 736s Getting block 15 of 15 736s Reserving size (8) for bucket 15 736s Calculating Z arrays for bucket 15 736s Entering block accumulator loop for bucket 15: 736s bucket 15: 10% 736s bucket 15: 20% 736s bucket 15: 30% 736s bucket 15: 40% 736s bucket 15: 50% 736s bucket 15: 60% 736s bucket 15: 70% 736s bucket 15: 80% 736s bucket 15: 90% 736s bucket 15: 100% 736s Sorting block of length 5 for bucket 15 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 6 for bucket 15 736s Exited Ebwt loop 736s fchr[A]: 0 736s fchr[C]: 27 736s fchr[G]: 51 736s fchr[T]: 67 736s fchr[$]: 86 736s Exiting Ebwt::buildToDisk() 736s Returning from initFromVector 736s Wrote 4194647 bytes to primary EBWT file: /tmp/Sim.pm.WCUbbuUs.1.bt2.tmp 736s Wrote 92 bytes to secondary EBWT file: /tmp/Sim.pm.WCUbbuUs.2.bt2.tmp 736s Re-opening _in1 and _in2 as input streams 736s Returning from Ebwt constructor 736s Headers: 736s len: 86 736s bwtLen: 87 736s sz: 22 736s bwtSz: 22 736s lineRate: 6 736s offRate: 2 736s offMask: 0xfffffffc 736s ftabChars: 10 736s eftabLen: 20 736s eftabSz: 80 736s ftabLen: 1048577 736s ftabSz: 4194308 736s offsLen: 22 736s offsSz: 88 736s lineSz: 64 736s sideSz: 64 736s sideBwtSz: 48 736s sideBwtLen: 192 736s numSides: 1 736s numLines: 1 736s ebwtTotLen: 64 736s ebwtTotSz: 64 736s color: 0 736s reverse: 0 736s Total time for call to driver() for forward index: 00:00:00 736s Reading reference sizes 736s Time reading reference sizes: 00:00:00 736s Calculating joined length 736s Writing header 736s Reserving space for joined string 736s Joining reference sequences 736s Time to join reference sequences: 00:00:00 736s Time to reverse reference sequence: 00:00:00 736s bmax according to bmaxDivN setting: 10 736s Using parameters --bmax 8 --dcv 16 736s Doing ahead-of-time memory usage test 736s Passed! Constructing with these parameters: --bmax 8 --dcv 16 736s Constructing suffix-array element generator 736s Building DifferenceCoverSample 736s Building sPrime 736s Building sPrimeOrder 736s V-Sorting samples 736s V-Sorting samples time: 00:00:00 736s Allocating rank array 736s Ranking v-sort output 736s Ranking v-sort output time: 00:00:00 736s Invoking Larsson-Sadakane on ranks 736s Invoking Larsson-Sadakane on ranks time: 00:00:00 736s Sanity-checking and returning 736s Building samples 736s Reserving space for 26 sample suffixes 736s Generating random suffixes 736s QSorting 26 sample offsets, eliminating duplicates 736s QSorting sample offsets, eliminating duplicates time: 00:00:00 736s Multikey QSorting 24 samples 736s (Using difference cover) 736s Multikey QSorting samples time: 00:00:00 736s Calculating bucket sizes 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Split 1, merged 12; iterating... 736s Splitting and merging 736s Splitting and merging time: 00:00:00 736s Avg bucket size: 5.69231 (target: 7) 736s Converting suffix-array elements to index image 736s Allocating ftab, absorbFtab 736s Entering Ebwt loop 736s Getting block 1 of 13 736s Reserving size (8) for bucket 1 736s Calculating Z arrays for bucket 1 736s Entering block accumulator loop for bucket 1: 736s bucket 1: 10% 736s bucket 1: 20% 736s bucket 1: 30% 736s bucket 1: 40% 736s bucket 1: 50% 736s bucket 1: 60% 736s bucket 1: 70% 736s bucket 1: 80% 736s bucket 1: 90% 736s bucket 1: 100% 736s Sorting block of length 7 for bucket 1 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 8 for bucket 1 736s Getting block 2 of 13 736s Reserving size (8) for bucket 2 736s Calculating Z arrays for bucket 2 736s Entering block accumulator loop for bucket 2: 736s bucket 2: 10% 736s bucket 2: 20% 736s bucket 2: 30% 736s bucket 2: 40% 736s bucket 2: 50% 736s bucket 2: 60% 736s bucket 2: 70% 736s bucket 2: 80% 736s bucket 2: 90% 736s bucket 2: 100% 736s Sorting block of length 7 for bucket 2 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 8 for bucket 2 736s Getting block 3 of 13 736s Reserving size (8) for bucket 3 736s Calculating Z arrays for bucket 3 736s Entering block accumulator loop for bucket 3: 736s bucket 3: 10% 736s bucket 3: 20% 736s bucket 3: 30% 736s bucket 3: 40% 736s bucket 3: 50% 736s bucket 3: 60% 736s bucket 3: 70% 736s bucket 3: 80% 736s bucket 3: 90% 736s bucket 3: 100% 736s Sorting block of length 5 for bucket 3 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 6 for bucket 3 736s Getting block 4 of 13 736s Reserving size (8) for bucket 4 736s Calculating Z arrays for bucket 4 736s Entering block accumulator loop for bucket 4: 736s bucket 4: 10% 736s bucket 4: 20% 736s bucket 4: 30% 736s bucket 4: 40% 736s bucket 4: 50% 736s bucket 4: 60% 736s bucket 4: 70% 736s bucket 4: 80% 736s bucket 4: 90% 736s bucket 4: 100% 736s Sorting block of length 6 for bucket 4 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 7 for bucket 4 736s Getting block 5 of 13 736s Reserving size (8) for bucket 5 736s Calculating Z arrays for bucket 5 736s Entering block accumulator loop for bucket 5: 736s bucket 5: 10% 736s bucket 5: 20% 736s bucket 5: 30% 736s bucket 5: 40% 736s bucket 5: 50% 736s bucket 5: 60% 736s bucket 5: 70% 736s bucket 5: 80% 736s bucket 5: 90% 736s bucket 5: 100% 736s Sorting block of length 7 for bucket 5 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 8 for bucket 5 736s Getting block 6 of 13 736s Reserving size (8) for bucket 6 736s Calculating Z arrays for bucket 6 736s Entering block accumulator loop for bucket 6: 736s bucket 6: 10% 736s bucket 6: 20% 736s bucket 6: 30% 736s bucket 6: 40% 736s bucket 6: 50% 736s bucket 6: 60% 736s bucket 6: 70% 736s bucket 6: 80% 736s bucket 6: 90% 736s bucket 6: 100% 736s Sorting block of length 7 for bucket 6 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 8 for bucket 6 736s Getting block 7 of 13 736s Reserving size (8) for bucket 7 736s Calculating Z arrays for bucket 7 736s Entering block accumulator loop for bucket 7: 736s bucket 7: 10% 736s bucket 7: 20% 736s bucket 7: 30% 736s bucket 7: 40% 736s bucket 7: 50% 736s bucket 7: 60% 736s bucket 7: 70% 736s bucket 7: 80% 736s bucket 7: 90% 736s bucket 7: 100% 736s Sorting block of length 5 for bucket 7 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 6 for bucket 7 736s Getting block 8 of 13 736s Reserving size (8) for bucket 8 736s Calculating Z arrays for bucket 8 736s Entering block accumulator loop for bucket 8: 736s bucket 8: 10% 736s bucket 8: 20% 736s bucket 8: 30% 736s bucket 8: 40% 736s bucket 8: 50% 736s bucket 8: 60% 736s bucket 8: 70% 736s bucket 8: 80% 736s bucket 8: 90% 736s bucket 8: 100% 736s Sorting block of length 6 for bucket 8 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 7 for bucket 8 736s Getting block 9 of 13 736s Reserving size (8) for bucket 9 736s Calculating Z arrays for bucket 9 736s Entering block accumulator loop for bucket 9: 736s bucket 9: 10% 736s bucket 9: 20% 736s bucket 9: 30% 736s bucket 9: 40% 736s bucket 9: 50% 736s bucket 9: 60% 736s bucket 9: 70% 736s bucket 9: 80% 736s bucket 9: 90% 736s bucket 9: 100% 736s Sorting block of length 1 for bucket 9 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 2 for bucket 9 736s Getting block 10 of 13 736s Reserving size (8) for bucket 10 736s Calculating Z arrays for bucket 10 736s Entering block accumulator loop for bucket 10: 736s bucket 10: 10% 736s bucket 10: 20% 736s bucket 10: 30% 736s bucket 10: 40% 736s bucket 10: 50% 736s bucket 10: 60% 736s bucket 10: 70% 736s bucket 10: 80% 736s bucket 10: 90% 736s bucket 10: 100% 736s Sorting block of length 6 for bucket 10 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 7 for bucket 10 736s Getting block 11 of 13 736s Reserving size (8) for bucket 11 736s Calculating Z arrays for bucket 11 736s Entering block accumulator loop for bucket 11: 736s bucket 11: 10% 736s bucket 11: 20% 736s bucket 11: 30% 736s bucket 11: 40% 736s bucket 11: 50% 736s bucket 11: 60% 736s bucket 11: 70% 736s bucket 11: 80% 736s bucket 11: 90% 736s bucket 11: 100% 736s Sorting block of length 5 for bucket 11 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 6 for bucket 11 736s Getting block 12 of 13 736s Reserving size (8) for bucket 12 736s Calculating Z arrays for bucket 12 736s Entering block accumulator loop for bucket 12: 736s bucket 12: 10% 736s bucket 12: 20% 736s bucket 12: 30% 736s bucket 12: 40% 736s bucket 12: 50% 736s bucket 12: 60% 736s bucket 12: 70% 736s bucket 12: 80% 736s bucket 12: 90% 736s bucket 12: 100% 736s Sorting block of length 6 for bucket 12 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 7 for bucket 12 736s Getting block 13 of 13 736s Reserving size (8) for bucket 13 736s Calculating Z arrays for bucket 13 736s Entering block accumulator loop for bucket 13: 736s bucket 13: 10% 736s bucket 13: 20% 736s bucket 13: 30% 736s bucket 13: 40% 736s bucket 13: 50% 736s bucket 13: 60% 736s bucket 13: 70% 736s bucket 13: 80% 736s bucket 13: 90% 736s bucket 13: 100% 736s Sorting block of length 6 for bucket 13 736s (Using difference cover) 736s Sorting block time: 00:00:00 736s Returning block of 7 for bucket 13 736s Exited Ebwt loop 736s fchr[A]: 0 736s fchr[C]: 27 736s fchr[G]: 51 736s fchr[T]: 67 736s fchr[$]: 86 736s Exiting Ebwt::buildToDisk() 736s Returning from initFromVector 736s Wrote 4194647 bytes to primary EBWT file: /tmp/Sim.pm.WCUbbuUs.rev.1.bt2.tmp 736s Wrote 92 bytes to secondary EBWT file: /tmp/Sim.pm.WCUbbuUs.rev.2.bt2.tmp 736s Re-opening _in1 and _in2 as input streams 736s Returning from Ebwt constructor 736s Headers: 736s len: 86 736s bwtLen: 87 736s Renaming /tmp/Sim.pm.WCUbbuUs.3.bt2.tmp to /tmp/Sim.pm.WCUbbuUs.3.bt2 736s Renaming /tmp/Sim.pm.WCUbbuUs.4.bt2.tmp to /tmp/Sim.pm.WCUbbuUs.4.bt2 736s Renaming /tmp/Sim.pm.WCUbbuUs.1.bt2.tmp to /tmp/Sim.pm.WCUbbuUs.1.bt2 736s Renaming /tmp/Sim.pm.WCUbbuUs.2.bt2.tmp to /tmp/Sim.pm.WCUbbuUs.2.bt2 736s Renaming /tmp/Sim.pm.WCUbbuUs.rev.1.bt2.tmp to /tmp/Sim.pm.WCUbbuUs.rev.1.bt2 736s Renaming /tmp/Sim.pm.WCUbbuUs.rev.2.bt2.tmp to /tmp/Sim.pm.WCUbbuUs.rev.2.bt2 736s Built nucleotide index '/tmp/Sim.pm.WCUbbuUs' 736s Flattened IUPAC characters 736s Mutating sequence Sim.pm.2 736s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s sz: 22 736s bwtSz: 22 736s lineRate: 6 736s offRate: 2 736s offMask: 0xfffffffc 736s ftabChars: 10 736s eftabLen: 20 736s eftabSz: 80 736s ftabLen: 1048577 736s ftabSz: 4194308 736s offsLen: 22 736s offsSz: 88 736s lineSz: 64 736s sideSz: 64 736s sideBwtSz: 48 736s sideBwtLen: 192 736s numSides: 1 736s numLines: 1 736s ebwtTotLen: 64 736s ebwtTotSz: 64 736s color: 0 736s reverse: 1 736s Total time for backward call to driver() for mirror index: 00:00:00 736s Mutating sequence Sim.pm.1 736s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutated reference genome to subject genome 736s SNPs introduced: 8 736s Reference gaps introduced: 2 736s Read gaps introduced: 0 736s Rearrangements introduced: 0 736s Created read sampler 736s Sampling 98 reads 736s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 736s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 736s parsing sequence Sim.pm.1... 736s parsing sequence Sim.pm.2... 736s Parsed 94 reference bases 736s *** Run 1 of 100 736s /usr/bin/bowtie2 --mm --rdg 28.5976162770751 --rfg 35.8980924148755 --score-min L,9.48973767255792,2.11057412223835 --trim3 0 --n-ceil 0.680380989719361,1.15477634531259 --cp-ival 1 -M 2 --trim5 7 -R 3 --ma 9.53203205076173 --cp-min 2 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 736s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 736s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '3' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 736s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '6' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '16' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 736s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '23' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 736s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '24' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 736s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '37' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '42' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 736s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '44' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 736s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #2 of read '52' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 736s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '53' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 736s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '57' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 736s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '64' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 736s Read 50 alignments... 736s Read 100 alignments... 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 736s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '68' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 736s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '74' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 736s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #2 of read '82' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 736s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '83' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 736s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '97' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 736s 98 reads; of these: 736s 80 (81.63%) were paired; of these: 736s 78 (97.50%) aligned concordantly 0 times 736s 0 (0.00%) aligned concordantly exactly 1 time 736s 2 (2.50%) aligned concordantly >1 times 736s ---- 736s 78 pairs aligned concordantly 0 times; of these: 736s 0 (0.00%) aligned discordantly 1 time 736s ---- 736s 78 pairs aligned 0 times concordantly or discordantly; of these: 736s 156 mates make up the pairs; of these: 736s 147 (94.23%) aligned 0 times 736s 1 (0.64%) aligned exactly 1 time 736s 8 (5.13%) aligned >1 times 736s 18 (18.37%) were unpaired; of these: 736s 16 (88.89%) aligned 0 times 736s 0 (0.00%) aligned exactly 1 time 736s 2 (11.11%) aligned >1 times 736s 8.43% overall alignment rate 736s Read 150 alignments... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CC 736s CC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TTG 736s TTG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GCGTCAACACCT 736s GCGTCAACACCT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TGGC 736s TGGC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TTG 736s TTG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CTG 736s CTG 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GTCA 736s GTCA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TCA 736s TCA 736s Processing line... 736s Processing line... 736s CAA 736s CAA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s ATGCT 736s ATGCT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GCGT 736s GCGT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GAT 736s GAT 736s Processing line... 736s CA 736s CA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TC 736s TC 736s Processing line... 736s GCT 736s GCT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s --- Summary --- 736s Read 1 reference strings 736s Checked 15 alignments, 0 edits 736s --------------- 736s PASSED 736s ALSO checking that bowtie2 and bowtie2-align match up 736s /usr/bin/bowtie2 --mm --rdg 28.5976162770751 --rfg 35.8980924148755 --score-min L,9.48973767255792,2.11057412223835 --trim3 0 --n-ceil 0.680380989719361,1.15477634531259 --cp-ival 1 -M 2 --trim5 7 -R 3 --ma 9.53203205076173 --cp-min 2 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 736s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 736s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '3' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 736s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '6' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '16' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 736s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '23' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 736s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '24' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 736s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '37' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '42' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 736s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '44' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 736s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #2 of read '52' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 736s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '53' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 736s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '57' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 736s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '64' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 736s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '68' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 736s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '74' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 736s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 736s Warning: skipping mate #2 of read '82' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 736s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '83' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 736s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 736s Warning: skipping mate #1 of read '97' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 736s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 736s *** Run 2 of 100 736s /usr/bin/bowtie2 --trim5 2 -M 2 --cp-min 4 --mm --score-min L,7.28014203385081,4.05591769691231 --rfg 3.19690563238085,12.7232353596366 --rdg 41.4002544232745,6.96727528992035 --cp-ival 4 --local --mp 8.82769736198442,1.44922195336961 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 736s 98 reads; of these: 736s 80 (81.63%) were paired; of these: 736s 78 (97.50%) aligned concordantly 0 times 736s 0 (0.00%) aligned concordantly exactly 1 time 736s 2 (2.50%) aligned concordantly >1 times 736s ---- 736s 78 pairs aligned concordantly 0 times; of these: 736s 0 (0.00%) aligned discordantly 1 time 736s ---- 736s 78 pairs aligned 0 times concordantly or discordantly; of these: 736s 156 mates make up the pairs; of these: 736s 147 (94.23%) aligned 0 times 736s 1 (0.64%) aligned exactly 1 time 736s 8 (5.13%) aligned >1 times 736s 18 (18.37%) were unpaired; of these: 736s 16 (88.89%) aligned 0 times 736s 0 (0.00%) aligned exactly 1 time 736s 2 (11.11%) aligned >1 times 736s 8.43% overall alignment rate 736s Flattened IUPAC characters 736s Mutating sequence Sim.pm.1 736s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutating sequence Sim.pm.2 736s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutated reference genome to subject genome 736s SNPs introduced: 8 736s Reference gaps introduced: 0 736s Read gaps introduced: 0 736s Rearrangements introduced: 0 736s Created read sampler 736s Sampling 47 reads 736s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 736s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 736s parsing sequence Sim.pm.1... 736s parsing sequence Sim.pm.2... 736s Parsed 94 reference bases 736s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 736s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '6' because it was < 2 characters long 736s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '18' because it was < 2 characters long 736s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '31' because it was < 2 characters long 736s 47 reads; of these: 736s 47 (100.00%) were unpaired; of these: 736s 47 (100.00%) aligned 0 times 736s 0 (0.00%) aligned exactly 1 time 736s 0 (0.00%) aligned >1 times 736s 0.00% overall alignment rate 736s Read 50 alignments... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s --- Summary --- 736s Read 1 reference strings 736s Checked 0 alignments, 0 edits 736s --------------- 736s PASSED 736s ALSO checking that bowtie2 and bowtie2-align match up 736s /usr/bin/bowtie2 --trim5 2 -M 2 --cp-min 4 --mm --score-min L,7.28014203385081,4.05591769691231 --rfg 3.19690563238085,12.7232353596366 --rdg 41.4002544232745,6.96727528992035 --cp-ival 4 --local --mp 8.82769736198442,1.44922195336961 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 736s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 736s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '6' because it was < 2 characters long 736s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 736s Warning: skipping read '18' because it was < 2 characters long 736s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 736s Warning: skipping read '31' because it was < 2 characters long 736s 47 reads; of these: 736s 47 (100.00%) were unpaired; of these: 736s 47 (100.00%) aligned 0 times 736s 0 (0.00%) aligned exactly 1 time 736s 0 (0.00%) aligned >1 times 736s 0.00% overall alignment rate 736s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 736s Flattened IUPAC characters 736s Mutating sequence Sim.pm.1 736s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutating sequence Sim.pm.2 736s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 736s Finished SNPs 736s Finished ref gaps 736s Finished read gaps 736s Mutated reference genome to subject genome 736s SNPs introduced: 6 736s Reference gaps introduced: 0 736s Read gaps introduced: 1 736s Rearrangements introduced: 1 736s Created read sampler 736s Sampling 48 reads 736s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 736s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 736s parsing sequence Sim.pm.1... 736s parsing sequence Sim.pm.2... 736s Parsed 94 reference bases 736s *** Run 3 of 100 736s /usr/bin/bowtie2 -i C,11.6104701072397 --trim5 6 --cp-min 3 --ma 37.777648305567 --score-min L,1.03614353485042,5.13021659202334 --rfg 46.4932413496662 --rdg 32.3820634640173 --trim3 6 --cp-ival 1 --nofw -N 1 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '4' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 736s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '7' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 736s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '9' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 736s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '15' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 736s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '17' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 736s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '21' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 736s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '24' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '27' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 736s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '31' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 736s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '34' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 736s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '36' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 736s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '37' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '40' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 736s Warning: skipping read '41' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '41' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '42' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 736s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '46' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 736s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '47' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s /usr/bin/bowtie2 -i C,11.6104701072397 --trim5 6 --cp-min 3 --ma 37.777648305567 --score-min L,1.03614353485042,5.13021659202334 --rfg 46.4932413496662 --rdg 32.3820634640173 --trim3 6 --cp-ival 1 --nofw -N 1 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 736s 48 reads; of these: 736s 48 (100.00%) were unpaired; of these: 736s 41 (85.42%) aligned 0 times 736s 0 (0.00%) aligned exactly 1 time 736s 7 (14.58%) aligned >1 times 736s 14.58% overall alignment rate 736s Read 50 alignments... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s TT 736s TT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GGCGTCAACAC 736s GGCGTCAACAC 736s Processing line... 736s Processing line... 736s GGCGTCA 736s GGCGTCA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s GGCGTCAACAC 736s GGCGTCAACAC 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CAACACCT 736s CAACACCT 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s CCGAA 736s CCGAA 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s Processing line... 736s AC 736s AC 736s --- Summary --- 736s Read 1 reference strings 736s Checked 7 alignments, 0 edits 736s --------------- 736s PASSED 736s ALSO checking that bowtie2 and bowtie2-align match up 736s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 736s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 736s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '4' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 736s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '7' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 736s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '9' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 736s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '15' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 736s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '17' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 736s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '21' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 736s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '24' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 736s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '27' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 736s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '31' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 736s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '34' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 736s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '36' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 736s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '37' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 736s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '40' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 736s Warning: skipping read '41' because length (1) <= # seed mismatches (1) 736s Warning: skipping read '41' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 736s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '42' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 736s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 736s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '46' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 736s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 736s Warning: skipping read '47' because it was < 2 characters long 736s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 736s 48 reads; of these: 736s 48 (100.00%) were unpaired; of these: 736s 41 (85.42%) aligned 0 times 736s 0 (0.00%) aligned exactly 1 time 736s 7 (14.58%) aligned >1 times 736s 14.58% overall alignment rate 736s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 736s /usr/bin/bowtie2 -i C,11.6104701072397 --trim5 6 --cp-min 3 --ma 37.777648305567 --score-min L,1.03614353485042,5.13021659202334 --rfg 46.4932413496662 --rdg 32.3820634640173 --trim3 6 --cp-ival 1 --nofw -N 1 -q -p 4 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 736s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 737s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 737s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 737s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '4' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 737s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '7' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 737s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '9' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 737s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '15' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 737s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '17' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 737s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '21' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 737s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '24' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 737s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '27' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 737s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '31' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 737s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '34' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 737s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '36' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 737s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '37' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 737s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '40' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 737s Warning: skipping read '41' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '41' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 737s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '42' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 737s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '46' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 737s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '47' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 737s 48 reads; of these: 737s 48 (100.00%) were unpaired; of these: 737s 41 (85.42%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 7 (14.58%) aligned >1 times 737s 14.58% overall alignment rate 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 737s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 737s /usr/bin/bowtie2 -i C,11.6104701072397 --trim5 6 --cp-min 3 --ma 37.777648305567 --score-min L,1.03614353485042,5.13021659202334 --rfg 46.4932413496662 --rdg 32.3820634640173 --trim3 6 --cp-ival 1 --nofw -N 1 -q -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 737s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 737s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 737s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 737s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '4' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 737s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '7' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 737s Warning: skipping read '9' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '9' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 737s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '15' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 737s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '17' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 737s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '21' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 737s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '24' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 737s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '27' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 737s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '31' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 737s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '34' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 737s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '36' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 737s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '37' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 737s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '40' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 737s Warning: skipping read '41' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '41' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 737s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '42' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 737s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '46' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 737s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 737s Warning: skipping read '47' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 737s 48 reads; of these: 737s 48 (100.00%) were unpaired; of these: 737s 41 (85.42%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 7 (14.58%) aligned >1 times 737s 14.58% overall alignment rate 737s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.2 737s Introducing 7 SNPs, 1/1 ref/read gaps, and 1 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s *** Run 4 of 100 737s /usr/bin/bowtie2 --trim5 3 --cp-min 8 -a --mm --score-min L,7.50747386651825,6.10328414979351 --trim3 0 --mp 7.00953609720365,6.91128675614455 --cp-ival 1 --n-ceil 1.11440855950337,1.25043141529275 -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta 737s Mutating sequence Sim.pm.1 737s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 9 737s Reference gaps introduced: 1 737s Read gaps introduced: 1 737s Rearrangements introduced: 1 737s Created read sampler 737s Sampling 136 reads 737s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 737s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 94 reference bases 737s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 737s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 737s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '9' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 737s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '16' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 737s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '32' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 737s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '33' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 737s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '41' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 737s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '53' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 737s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '57' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 737s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '72' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 737s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '76' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 737s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '77' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 737s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '82' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 737s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '89' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 737s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '92' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 737s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '93' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 737s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '110' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 737s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '114' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 737s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '115' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 737s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '118' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 737s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '130' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 737s Read 50 alignments... 737s 136 Read 100 alignments... 737s Read 150 alignments... 737s reads; of these: 737s 136 (100.00%) were unpaired; of these: 737s 111 (81.62%) aligned 0 times 737s 13 (9.56%) aligned exactly 1 time 737s 12 (8.82%) aligned >1 times 737s 18.38% overall alignment rate 737s Read 200 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ACATTT 737s ACATTT 737s Processing line... 737s TGAACATGGA 737s TGAACATGGA 737s Processing line... 737s CCGAAA 737s CCGAAA 737s Processing line... 737s CCGAAA 737s CCGAAA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CCGA 737s CCGA 737s Processing line... 737s CCGA 737s CCGA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ACATG 737s ACATG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TGGCG 737s TGGCG 737s Processing line... 737s TGGCG 737s TGGCG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ATAAC 737s ATAAC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s TGGATTCAATCATA 737s TGGATTCAATCATA 737s Processing line... 737s Processing line... 737s Processing line... 737s GATTC 737s GATTC 737s Processing line... 737s Processing line... 737s Processing line... 737s ACATGGATTC 737s ACATGGATTC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GA 737s GA 737s Processing line... 737s TC 737s TC 737s Processing line... 737s TC 737s TC 737s Processing line... 737s GA 737s GA 737s Processing line... 737s GA 737s GA 737s Processing line... 737s GA 737s GA 737s Processing line... 737s TC 737s TC 737s Processing line... 737s TC 737s TC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s ATG 737s ATG 737s Processing line... 737s CAT 737s CAT 737s Processing line... 737s AACACCTG 737s AACACCTG 737s Processing line... 737s AACACCTG 737s AACACCTG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ATTCAATCA 737s ATTCAATCA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GAACATGGATTCAAT 737s GAACATGGATTCAAT 737s Processing line... 737s AACACA 737s AACACA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s Processing line... 737s ATTC 737s ATTC 737s Processing line... 737s Processing line... 737s TGCT 737s TGCT 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s AACATGGATTCAATCATAA 737s AACATGGATTCAATCATAA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s TG 737s TG 737s Processing line... 737s CA 737s CA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CG 737s CG 737s Processing line... 737s CG 737s CG 737s Processing line... 737s CG 737s CG 737s Processing line... 737s CG 737s CG 737s Processing line... 737s CG 737s CG 737s Processing line... 737s CG 737s CG 737s Processing line... 737s CG 737s CG 737s Processing line... 737s CG 737s CG 737s Processing line... 737s Processing line... 737s Processing line... 737s TT 737s TT 737s Processing line... 737s /usr/bin/bowtie2 --trim5 3 --cp-min 8 -a --mm --score-min L,7.50747386651825,6.10328414979351 --trim3 0 --mp 7.00953609720365,6.91128675614455 --cp-ival 1 --n-ceil 1.11440855950337,1.25043141529275 -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 737s TT 737s TT 737s Processing line... 737s AA 737s AA 737s Processing line... 737s AA 737s AA 737s Processing line... 737s AA 737s AA 737s Processing line... 737s AA 737s AA 737s Processing line... 737s AA 737s AA 737s Processing line... 737s TT 737s TT 737s Processing line... 737s AA 737s AA 737s Processing line... 737s AA 737s AA 737s Processing line... 737s TT 737s TT 737s Processing line... 737s TT 737s TT 737s Processing line... 737s AA 737s AA 737s Processing line... 737s AA 737s AA 737s --- Summary --- 737s Read 1 reference strings 737s Checked 108 alignments, 0 edits 737s --------------- 737s PASSED 737s ALSO checking that bowtie2 and bowtie2-align match up 737s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 737s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 737s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '9' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 737s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '16' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 737s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '32' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 737s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '33' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 737s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '41' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 737s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '53' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 737s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '57' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 737s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '72' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 737s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '76' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 737s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '77' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 737s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 737s /usr/bin/bowtie2 --trim5 3 --cp-min 8 -a --mm --score-min L,7.50747386651825,6.10328414979351 --trim3 0 --mp 7.00953609720365,6.91128675614455 --cp-ival 1 --n-ceil 1.11440855950337,1.25043141529275 -f -p 4 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 737s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 737s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '82' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 737s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '89' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 737s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '92' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 737s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '93' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 737s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '110' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 737s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '114' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 737s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '115' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 737s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '118' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 737s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '130' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 737s 136 reads; of these: 737s 136 (100.00%) were unpaired; of these: 737s 111 (81.62%) aligned 0 times 737s 13 (9.56%) aligned exactly 1 time 737s 12 (8.82%) aligned >1 times 737s 18.38% overall alignment rate 737s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 737s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 737s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 737s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '9' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 737s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '16' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 737s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '32' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 737s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '33' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 737s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '41' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 737s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '53' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 737s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '57' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 737s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '72' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 737s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '76' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 737s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '77' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 737s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '82' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 737s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '89' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 737s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '92' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 737s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '93' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 737s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '110' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 737s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '114' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 737s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '115' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 737s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '118' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 737s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 737s Warning: skipping read '130' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 737s 136 reads; of these: 737s 136 (100.00%) were unpaired; of these: 737s 111 (81.62%) aligned 0 times 737s 13 (9.56%) aligned exactly 1 time 737s 12 (8.82%) aligned >1 times 737s 18.38% overall alignment rate 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 737s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.1 737s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.2 737s Introducing 5 SNPs, 2/0 ref/read gaps, and 2 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 7 737s Reference gaps introduced: 2 737s Read gaps introduced: 0 737s Rearrangements introduced: 3 737s Created read sampler 737s Sampling 55 reads 737s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 737s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 94 reference bases 737s *** Run 5 of 100 737s /usr/bin/bowtie2 --norc -i C,4.03491447352233,4.71437223009842 -k 3 --cp-min 4 --rfg 38.8067224140146 --score-min L,4.80565536184269,2.04770800613574 --gbar 5 --mm -N 1 -L18 --nofw --local --cp-ival 1 --trim3 0 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 737s Warning: skipping read '15' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '15' because it was < 2 characters long 737s Warning: skipping read '16' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '16' because it was < 2 characters long 737s Warning: skipping read '47' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '47' because it was < 2 characters long 737s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '48' because it was < 2 characters long 737s 55 reads; of these: 737s 55 (100.00%) were unpaired; of these: 737s 55 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 0.00% overall alignment rate 737s Read 50 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s /usr/bin/bowtie2 --norc -i C,4.03491447352233,4.71437223009842 -k 3 --cp-min 4 --rfg 38.8067224140146 --score-min L,4.80565536184269,2.04770800613574 --gbar 5 --mm -N 1 -L18 --nofw --local --cp-ival 1 --trim3 0 -r -p 3 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 0 alignments, 0 edits 737s --------------- 737s PASSED 737s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 737s Warning: skipping read '15' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '15' because it was < 2 characters long 737s Warning: skipping read '16' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '16' because it was < 2 characters long 737s Warning: skipping read '47' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '47' because it was < 2 characters long 737s Warning: skipping read '48' because length (1) <= # seed mismatches (1) 737s Warning: skipping read '48' because it was < 2 characters long 737s 55 reads; of these: 737s 55 (100.00%) were unpaired; of these: 737s 55 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 0.00% overall alignment rate 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 737s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.1 737s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.2 737s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 7 737s Reference gaps introduced: 0 737s Read gaps introduced: 0 737s Rearrangements introduced: 0 737s Created read sampler 737s Sampling 143 reads 737s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 737s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 94 reference bases 737s *** Run 6 of 100 737s /usr/bin/bowtie2 -N 0 -L28 --mp 7.59402994927603,6.33106874355154 --cp-ival 1 -D 17 --rfg 36.6575272432015 --score-min L,3.34547634439799,2.57698387282138 --gbar 2 --mm --cp-min 5 -R 2 -k 8 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 737s Read 50 alignments... 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 737s Warning: skipping mate #2 of read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 737s Read 100 alignments... 737s Read 150 alignments... 737s Read 200 alignments... 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 737s 143 reads; of these: 737s 143 (100.00%) were paired; of these: 737s 143 (100.00%) aligned concordantly 0 times 737s 0 (0.00%) aligned concordantly exactly 1 time 737s 0 (0.00%) aligned concordantly >1 times 737s ---- 737s 143 pairs aligned concordantly 0 times; of these: 737s 0 (0.00%) aligned discordantly 1 time 737s ---- 737s 143 pairs aligned 0 times concordantly or discordantly; of these: 737s 286 mates make up the pairs; of these: 737s 260 (90.91%) aligned 0 times 737s 2 (0.70%) aligned exactly 1 time 737s 24 (8.39%) aligned >1 times 737s 9.09% overall alignment rate 737s Read 250 alignments... 737s Read 300 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CTG 737s CTG 737s Processing line... 737s CTG 737s CTG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s GT 737s GT 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s AT 737s AT 737s Processing line... 737s AT 737s AT 737s Processing line... 737s AT 737s AT 737s Processing line... 737s AT 737s AT 737s Processing line... 737s AT 737s AT 737s Processing line... 737s AT 737s AT 737s Processing line... 737s AT 737s AT 737s Processing line... 737s AT 737s AT 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s AACAC 737s AACAC 737s Processing line... 737s AACAC 737s AACAC 737s Processing line... 737s AACAC 737s AACAC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TGGCGTCAA 737s TGGCGTCAA 737s Processing line... 737s TGGCGTCAA 737s TGGCGTCAA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ACC 737s ACC 737s Processing line... 737s ACC 737s ACC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s AC 737s AC 737s Processing line... 737s GT 737s GT 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s GT 737s GT 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s AC 737s AC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CGAA 737s CGAA 737s Processing line... 737s CGAA 737s CGAA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ACACCTG 737s ACACCTG 737s Processing line... 737s ACACCTG 737s ACACCTG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CAACACCTG 737s CAACACCTG 737s Processing line... 737s CAACACCTG 737s CAACACCTG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s GC 737s GC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s AACACCTG 737s AACACCTG 737s Processing line... 737s AACACCTG 737s AACACCTG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GTCAACACCTG 737s GTCAACACCTG 737s Processing line... 737s GTCAACACCTG 737s GTCAACACCTG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CC 737s CC 737s Processing line... 737s CC 737s CC 737s Processing line... 737s CC 737s CC 737s Processing line... 737s CC 737s CC 737s Processing line... 737s CC 737s CC 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s GG 737s GG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GTC 737s GTC 737s Processing line... 737s GTC 737s GTC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ACATGGATTCAAT 737s ACATGGATTCAAT 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TTG 737s TTG 737s Processing line... 737s CAA 737s CAA 737s Processing line... 737s TTG 737s TTG 737s Processing line... 737s CAA 737s CAA 737s Processing line... 737s CAA 737s CAA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s GGCGTCAACA 737s GGCGTCAACA 737s Processing line... 737s GGCGTCAACA 737s GGCGTCAACA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TGCTA 737s TGCTA 737s Processing line... 737s GCGTCAACACC 737s GCGTCAACACC 737s Processing line... 737s GCGTCAACACC 737s GCGTCAACACC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CCC 737s CCC 737s Processing line... 737s CCC 737s CCC 737s Processing line... 737s Processing line... 737s /usr/bin/bowtie2 -N 0 -L28 --mp 7.59402994927603,6.33106874355154 --cp-ival 1 -D 17 --rfg 36.6575272432015 --score-min L,3.34547634439799,2.57698387282138 --gbar 2 --mm --cp-min 5 -R 2 -k 8 --qseq -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 737s Processing line... 737s Processing line... 737s TCAACACC 737s TCAACACC 737s Processing line... 737s TCAACACC 737s TCAACACC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s TTGGC 737s TTGGC 737s Processing line... 737s TTGGC 737s TTGGC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s ACACCTG 737s ACACCTG 737s Processing line... 737s ACACCTG 737s ACACCTG 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CGAA 737s CGAA 737s Processing line... 737s CGAA 737s CGAA 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s CGTCAACACC 737s CGTCAACACC 737s Processing line... 737s CGTCAACACC 737s CGTCAACACC 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 82 alignments, 0 edits 737s --------------- 737s PASSED 737s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 737s Warning: skipping mate #2 of read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 737s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 737s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 737s 143 reads; of these: 737s 143 (100.00%) were paired; of these: 737s 143 (100.00%) aligned concordantly 0 times 737s 0 (0.00%) aligned concordantly exactly 1 time 737s 0 (0.00%) aligned concordantly >1 times 737s ---- 737s 143 pairs aligned concordantly 0 times; of these: 737s 0 (0.00%) aligned discordantly 1 time 737s ---- 737s 143 pairs aligned 0 times concordantly or discordantly; of these: 737s 286 mates make up the pairs; of these: 737s 260 (90.91%) aligned 0 times 737s 2 (0.70%) aligned exactly 1 time 737s 24 (8.39%) aligned >1 times 737s 9.09% overall alignment rate 737s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.2 737s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.1 737s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 6 737s Reference gaps introduced: 0 737s Read gaps introduced: 1 737s Rearrangements introduced: 0 737s Created read sampler 737s Sampling 65 reads 737s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 737s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 94 reference bases 737s *** Run 7 of 100 737s /usr/bin/bowtie2 --rdg 41.7008236821601,7.49180788537658 --score-min L,2.9005448108289,3.43812396295394 --gbar 5 --mm --mp 4.0807169079133,2.57651517773224 --local --cp-ival 2 --trim3 4 --trim5 7 --cp-min 3 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 737s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '9' because it was < 2 characters long 737s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '12' because it was < 2 characters long 737s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '16' because it was < 2 characters long 737s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '22' because it was < 2 characters long 737s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '23' because it was < 2 characters long 737s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '28' because it was < 2 characters long 737s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '30' because it was < 2 characters long 737s Warning: skipping mate #2 of read '30' because it was < 2 characters long 737s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '32' because it was < 2 characters long 737s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '34' because it was < 2 characters long 737s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '35' because it was < 2 characters long 737s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '39' because it was < 2 characters long 737s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '42' because it was < 2 characters long 737s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '45' because it was < 2 characters long 737s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '55' because it was < 2 characters long 737s Read 50 alignments... 737s 65 reads; of these: 737s 54 (83.08%) were paired; of these: 737s 54 (100.00%) aligned concordantly 0 times 737s 0 (0.00%) aligned concordantly exactly 1 time 737s 0 (0.00%) aligned concordantly >1 times 737s ---- 737s 54 pairs aligned concordantly 0 times; of these: 737s 0 (0.00%) aligned discordantly 1 time 737s ---- 737s 54 pairs aligned 0 times concordantly or discordantly; of these: 737s 108 mates make up the pairs; of these: 737s 108 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 11 (16.92%) were unpaired; of these: 737s 11 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 0.00% overall alignment rate 737s Read 100 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 0 alignments, 0 edits 737s --------------- 737s PASSED 737s ALSO checking that bowtie2 and bowtie2-align match up 737s /usr/bin/bowtie2 --rdg 41.7008236821601,7.49180788537658 --score-min L,2.9005448108289,3.43812396295394 --gbar 5 --mm --mp 4.0807169079133,2.57651517773224 --local --cp-ival 2 --trim3 4 --trim5 7 --cp-min 3 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 737s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '9' because it was < 2 characters long 737s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '12' because it was < 2 characters long 737s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '16' because it was < 2 characters long 737s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '22' because it was < 2 characters long 737s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '23' because it was < 2 characters long 737s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '28' because it was < 2 characters long 737s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '30' because it was < 2 characters long 737s Warning: skipping mate #2 of read '30' because it was < 2 characters long 737s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 737s Warning: skipping read '32' because it was < 2 characters long 737s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '34' because it was < 2 characters long 737s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '35' because it was < 2 characters long 737s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '39' because it was < 2 characters long 737s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '42' because it was < 2 characters long 737s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '45' because it was < 2 characters long 737s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '55' because it was < 2 characters long 737s 65 reads; of these: 737s 54 (83.08%) were paired; of these: 737s 54 (100.00%) aligned concordantly 0 times 737s 0 (0.00%) aligned concordantly exactly 1 time 737s 0 (0.00%) aligned concordantly >1 times 737s ---- 737s 54 pairs aligned concordantly 0 times; of these: 737s 0 (0.00%) aligned discordantly 1 time 737s ---- 737s 54 pairs aligned 0 times concordantly or discordantly; of these: 737s 108 mates make up the pairs; of these: 737s 108 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 11 (16.92%) were unpaired; of these: 737s 11 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 0.00% overall alignment rate 737s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.2 737s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.1 737s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 4 737s Reference gaps introduced: 0 737s Read gaps introduced: 1 737s Rearrangements introduced: 0 737s Created read sampler 737s Sampling 102 reads 737s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 737s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 94 reference bases 737s *** Run 8 of 100 737s /usr/bin/bowtie2 --mp 9.80778621400792,2.22360761137989 --nofw --local --cp-ival 2 -D 14 --n-ceil 0.574814730956802,0.0464344476102516 --rfg 16.2828944083518,13.4616391217519 --score-min L,5.4916627867107,9.95472073934566 --mm --cp-min 4 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 737s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '10' because it was < 2 characters long 737s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '16' because it was < 2 characters long 737s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '21' because it was < 2 characters long 737s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '41' because it was < 2 characters long 737s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '45' because it was < 2 characters long 737s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '58' because it was < 2 characters long 737s Warning: skipping mate #2 of read '92' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '92' because it was < 2 characters long 737s Read 50 alignments... 737s Read 100 alignments... 737s 102 reads; of these: 737s 102 (100.00%) were paired; of these: 737s 102 (100.00%) aligned concordantly 0 times 737s 0 (0.00%) aligned concordantly exactly 1 time 737s 0 (0.00%) aligned concordantly >1 times 737s ---- 737s 102 pairs aligned concordantly 0 times; of these: 737s 0 (0.00%) aligned discordantly 1 time 737s ---- 737s 102 pairs aligned 0 times concordantly or discordantly; of these: 737s 204 mates make up the pairs; of these: 737s 204 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 0.00% overall alignment rate 737s Read 150 alignments... 737s Read 200 alignments... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing 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line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s Processing line... 737s --- Summary --- 737s Read 1 reference strings 737s Checked 0 alignments, 0 edits 737s --------------- 737s PASSED 737s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 737s /usr/bin/bowtie2 --mp 9.80778621400792,2.22360761137989 --nofw --local --cp-ival 2 -D 14 --n-ceil 0.574814730956802,0.0464344476102516 --rfg 16.2828944083518,13.4616391217519 --score-min L,5.4916627867107,9.95472073934566 --mm --cp-min 4 -r -p 3 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 737s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '10' because it was < 2 characters long 737s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #1 of read '16' because it was < 2 characters long 737s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '21' because it was < 2 characters long 737s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '41' because it was < 2 characters long 737s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '45' because it was < 2 characters long 737s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '58' because it was < 2 characters long 737s Warning: skipping mate #2 of read '92' because length (1) <= # seed mismatches (0) 737s Warning: skipping mate #2 of read '92' because it was < 2 characters long 737s 102 reads; of these: 737s 102 (100.00%) were paired; of these: 737s 102 (100.00%) aligned concordantly 0 times 737s 0 (0.00%) aligned concordantly exactly 1 time 737s 0 (0.00%) aligned concordantly >1 times 737s ---- 737s 102 pairs aligned concordantly 0 times; of these: 737s 0 (0.00%) aligned discordantly 1 time 737s ---- 737s 102 pairs aligned 0 times concordantly or discordantly; of these: 737s 204 mates make up the pairs; of these: 737s 204 (100.00%) aligned 0 times 737s 0 (0.00%) aligned exactly 1 time 737s 0 (0.00%) aligned >1 times 737s 0.00% overall alignment rate 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 737s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 737s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 737s Flattened IUPAC characters 737s Mutating sequence Sim.pm.2 737s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutating sequence Sim.pm.1 737s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 737s Finished SNPs 737s Finished ref gaps 737s Finished read gaps 737s Mutated reference genome to subject genome 737s SNPs introduced: 1 737s Reference gaps introduced: 0 737s Read gaps introduced: 0 737s Rearrangements introduced: 0 737s Created read sampler 737s Sampling 110 reads 737s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 737s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 737s parsing sequence Sim.pm.1... 737s parsing sequence Sim.pm.2... 737s Parsed 94 reference bases 737s *** Run 9 of 100 737s /usr/bin/bowtie2 --cp-ival 2 --local --n-ceil 0.159602615780301,0.565540408981468 --mp 9.86660892500624,8.68882579195788 --nofw --trim3 7 --rfg 45.5875747534185 --score-min L,6.87567120996865,8.76455145794287 --mm --cp-min 2 -R 1 --norc -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 738s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '9' because it was < 2 characters long 738s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '16' because it was < 2 characters long 738s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '19' because it was < 2 characters long 738s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '23' because it was < 2 characters long 738s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '24' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '37' because it was < 2 characters long 738s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '39' because it was < 2 characters long 738s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '42' because it was < 2 characters long 738s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '44' because it was < 2 characters long 738s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '46' because it was < 2 characters long 738s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '47' because it was < 2 characters long 738s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '50' because it was < 2 characters long 738s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '52' because it was < 2 characters long 738s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '54' because it was < 2 characters long 738s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '57' because it was < 2 characters long 738s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '60' because it was < 2 characters long 738s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '64' because it was < 2 characters long 738s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '70' because it was < 2 characters long 738s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '71' because it was < 2 characters long 738s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '78' because it was < 2 characters long 738s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '85' because it was < 2 characters long 738s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '94' because it was < 2 characters long 738s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '109' because it was < 2 characters long 738s 110 reads; of these: 738s 110 (100.00%) were unpaired; of these: 738s 110 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s Read 50 alignments... 738s Read 100 alignments... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 0 alignments, 0 edits 738s --------------- 738s PASSED 738s ALSO checking that bowtie2 and bowtie2-align match up 738s /usr/bin/bowtie2 --cp-ival 2 --local --n-ceil 0.159602615780301,0.565540408981468 --mp 9.86660892500624,8.68882579195788 --nofw --trim3 7 --rfg 45.5875747534185 --score-min L,6.87567120996865,8.76455145794287 --mm --cp-min 2 -R 1 --norc -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 738s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '9' because it was < 2 characters long 738s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '16' because it was < 2 characters long 738s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '19' because it was < 2 characters long 738s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '23' because it was < 2 characters long 738s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '24' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '37' because it was < 2 characters long 738s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '39' because it was < 2 characters long 738s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '42' because it was < 2 characters long 738s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '44' because it was < 2 characters long 738s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '46' because it was < 2 characters long 738s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '47' because it was < 2 characters long 738s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '50' because it was < 2 characters long 738s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '52' because it was < 2 characters long 738s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '54' because it was < 2 characters long 738s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '57' because it was < 2 characters long 738s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '60' because it was < 2 characters long 738s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '64' because it was < 2 characters long 738s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '70' because it was < 2 characters long 738s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '71' because it was < 2 characters long 738s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '78' because it was < 2 characters long 738s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '85' because it was < 2 characters long 738s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '94' because it was < 2 characters long 738s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '109' because it was < 2 characters long 738s 110 reads; of these: 738s 110 (100.00%) were unpaired; of these: 738s 110 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 738s /usr/bin/bowtie2 --cp-ival 2 --local --n-ceil 0.159602615780301,0.565540408981468 --mp 9.86660892500624,8.68882579195788 --nofw --trim3 7 --rfg 45.5875747534185 --score-min L,6.87567120996865,8.76455145794287 --mm --cp-min 2 -R 1 --norc -r -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 738s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 738s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '9' because it was < 2 characters long 738s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '16' because it was < 2 characters long 738s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '19' because it was < 2 characters long 738s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '23' because it was < 2 characters long 738s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '24' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '37' because it was < 2 characters long 738s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '39' because it was < 2 characters long 738s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '42' because it was < 2 characters long 738s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '44' because it was < 2 characters long 738s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '46' because it was < 2 characters long 738s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '47' because it was < 2 characters long 738s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '50' because it was < 2 characters long 738s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '52' because it was < 2 characters long 738s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '54' because it was < 2 characters long 738s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '57' because it was < 2 characters long 738s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '60' because it was < 2 characters long 738s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '64' because it was < 2 characters long 738s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '70' because it was < 2 characters long 738s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '71' because it was < 2 characters long 738s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '78' because it was < 2 characters long 738s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '85' because it was < 2 characters long 738s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '94' because it was < 2 characters long 738s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '109' because it was < 2 characters long 738s 110 reads; of these: 738s 110 (100.00%) were unpaired; of these: 738s 110 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.2 738s Introducing 3 SNPs, 1/1 ref/read gaps, and 1 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.1 738s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 6 738s Reference gaps introduced: 1 738s Read gaps introduced: 1 738s Rearrangements introduced: 1 738s Created read sampler 738s Sampling 104 reads 738s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 738s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 94 reference bases 738s *** Run 10 of 100 738s /usr/bin/bowtie2 --cp-min 5 --norc --np 10 -M 2 -N 1 -L17 --mp 9.88439436870326,9.16858068962086 --cp-ival 1 --local --score-min L,3.25349634864702,8.28601344922145 --rdg 25.2686343872146,8.55246236871896 --mm -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 738s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 738s Warning: skipping read '45' because length (1) <= # seed mismatches (1) 738s Warning: skipping read '45' because it was < 2 characters long 738s Warning: skipping read '50' because length (1) <= # seed mismatches (1) 738s Warning: skipping read '50' because it was < 2 characters long 738s 104 reads; of these: 738s 104 (100.00%) were unpaired; of these: 738s 104 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s Read 50 alignments... 738s Read 100 alignments... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 0 alignments, 0 edits 738s --------------- 738s PASSED 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.1 738s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.2 738s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 6 738s Reference gaps introduced: 0 738s Read gaps introduced: 1 738s Rearrangements introduced: 0 738s Created read sampler 738s Sampling 47 reads 738s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 738s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 94 reference bases 738s *** Run 11 of 100 738s /usr/bin/bowtie2 -i C,0.186352758128189 --trim5 9 --ma 13.7340276741387 --cp-min 6 --score-min L,7.5726742673094,3.72685293284361 --rfg 17.553957177832 --gbar 1 -a --mm --mp 7.94855987915191,2.77270296247664 --n-ceil 0.471792786429816,0.0539180576256639 --cp-ival 2 -D 27 --trim3 6 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 738s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 738s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 738s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 738s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 738s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 738s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 738s 47 reads; of these: 738s 37 (78.72%) were paired; of these: 738s 37 (100.00%) aligned concordantly 0 times 738s 0 (0.00%) aligned concordantly exactly 1 time 738s 0 (0.00%) aligned concordantly >1 times 738s ---- 738s 37 pairs aligned concordantly 0 times; of these: 738s 0 (0.00%) aligned discordantly 1 time 738s ---- 738s 37 pairs aligned 0 times concordantly or discordantly; of these: 738s 74 mates make up the pairs; of these: 738s 73 (98.65%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 1 (1.35%) aligned >1 times 738s 10 (21.28%) were unpaired; of these: 738s 9 (90.00%) aligned 0 times 738s 1 (10.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 2.38% overall alignment rate 738s Read 50 alignments... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GTC 738s GTC 738s Processing line... 738s GTC 738s GTC 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GCT 738s GCT 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 3 alignments, 0 edits 738s --------------- 738s PASSED 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.1 738s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.2 738s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 5 738s Reference gaps introduced: 0 738s Read gaps introduced: 1 738s Rearrangements introduced: 1 738s Created read sampler 738s Sampling 68 reads 738s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 738s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 94 reference bases 738s *** Run 12 of 100 738s /usr/bin/bowtie2 --cp-ival 1 --local --mp 9.02759972137678,5.99928177610922 --gbar 1 --rdg 27.9588434633341 --rfg 1.21434993307094 --score-min L,1.40123960427258,4.56586178862408 --cp-min 2 --np 3 -k 5 --trim5 8 -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta 738s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '2' because it was < 2 characters long 738s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '3' because it was < 2 characters long 738s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '16' because it was < 2 characters long 738s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '19' because it was < 2 characters long 738s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '22' because it was < 2 characters long 738s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '23' because it was < 2 characters long 738s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '28' because it was < 2 characters long 738s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '31' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '33' because it was < 2 characters long 738s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '37' because it was < 2 characters long 738s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '39' because it was < 2 characters long 738s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '41' because it was < 2 characters long 738s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '46' because it was < 2 characters long 738s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '47' because it was < 2 characters long 738s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '48' because it was < 2 characters long 738s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '55' because it was < 2 characters long 738s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '59' because it was < 2 characters long 738s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '63' because it was < 2 characters long 738s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '65' because it was < 2 characters long 738s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '66' because it was < 2 characters long 738s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '67' because it was < 2 characters long 738s 68 reads; of these: 738s 68 (100.00%) were unpaired; of these: 738s 68 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s Read 50 alignments... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s /usr/bin/bowtie2 --cp-ival 1 --local --mp 9.02759972137678,5.99928177610922 --gbar 1 --rdg 27.9588434633341 --rfg 1.21434993307094 --score-min L,1.40123960427258,4.56586178862408 --cp-min 2 --np 3 -k 5 --trim5 8 -f -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 0 alignments, 0 edits 738s --------------- 738s PASSED 738s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 738s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '2' because it was < 2 characters long 738s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '3' because it was < 2 characters long 738s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '16' because it was < 2 characters long 738s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '19' because it was < 2 characters long 738s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '22' because it was < 2 characters long 738s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '23' because it was < 2 characters long 738s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '28' because it was < 2 characters long 738s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '31' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '33' because it was < 2 characters long 738s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '34' because it was < 2 characters long 738s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '37' because it was < 2 characters long 738s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '39' because it was < 2 characters long 738s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '41' because it was < 2 characters long 738s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '46' because it was < 2 characters long 738s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '47' because it was < 2 characters long 738s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '48' because it was < 2 characters long 738s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '55' because it was < 2 characters long 738s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '59' because it was < 2 characters long 738s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '63' because it was < 2 characters long 738s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '65' because it was < 2 characters long 738s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '66' because it was < 2 characters long 738s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '67' because it was < 2 characters long 738s 68 reads; of these: 738s 68 (100.00%) were unpaired; of these: 738s 68 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.2 738s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.1 738s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 7 738s Reference gaps introduced: 0 738s Read gaps introduced: 2 738s Rearrangements introduced: 0 738s Created read sampler 738s Sampling 113 reads 738s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 738s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 94 reference bases 738s *** Run 13 of 100 738s /usr/bin/bowtie2 --trim5 2 --cp-min 9 --ma 23.8136389149163 -R 3 --gbar 9 --score-min L,7.64300987061851,1.37980631845237 --cp-ival 2 --nofw --mp 7.35007857473413,2.97039739018482 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 738s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 738s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '56' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 738s Read 50 alignments... 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 738s Warning: skipping mate #2 of read '67' because length (1) <= # seed mismatches (0) 738s Warning: skipping mate #2 of read '67' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 738s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '84' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 738s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 738s Warning: skipping mate #2 of read '89' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 738s Read 100 alignments... 738s Read 150 alignments... 738s 113 reads; of these: 738s 111 (98.23%) were paired; of these: 738s 111 (100.00%) aligned concordantly 0 times 738s 0 (0.00%) aligned concordantly exactly 1 time 738s 0 (0.00%) aligned concordantly >1 times 738s ---- 738s 111 pairs aligned concordantly 0 times; of these: 738s 0 (0.00%) aligned discordantly 1 time 738s ---- 738s 111 pairs aligned 0 times concordantly or discordantly; of these: 738s 222 mates make up the pairs; of these: 738s 206 (92.79%) aligned 0 times 738s 2 (0.90%) aligned exactly 1 time 738s 14 (6.31%) aligned >1 times 738s 2 (1.77%) were unpaired; of these: 738s 1 (50.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 1 (50.00%) aligned >1 times 738s 7.59% overall alignment rate 738s Read 200 alignments... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s AC 738s AC 738s Processing line... 738s GC 738s GC 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GGCG 738s GGCG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GC 738s GC 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s TTT 738s TTT 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GAT 738s GAT 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s TG 738s TG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s GC 738s GC 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s TCAACAC 738s TCAACAC 738s Processing line... 738s Processing line... 738s TTGGCGT 738s TTGGCGT 738s Processing line... 738s Processing line... 738s ACA 738s ACA 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s ATG 738s ATG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s CCCGAAA 738s CCCGAAA 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s AAC 738s AAC 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s CAC 738s CAC 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s AC 738s AC 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s TTGGCG 738s TTGGCG 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 17 alignments, 0 edits 738s --------------- 738s PASSED 738s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 738s /usr/bin/bowtie2 --trim5 2 --cp-min 9 --ma 23.8136389149163 -R 3 --gbar 9 --score-min L,7.64300987061851,1.37980631845237 --cp-ival 2 --nofw --mp 7.35007857473413,2.97039739018482 -r -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 738s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 738s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '56' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 738s Warning: skipping mate #2 of read '67' because length (1) <= # seed mismatches (0) 738s Warning: skipping mate #2 of read '67' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 738s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 738s Warning: skipping mate #1 of read '84' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 738s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 738s Warning: skipping mate #2 of read '89' because it was < 2 characters long 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 738s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 738s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 738s 113 reads; of these: 738s 111 (98.23%) were paired; of these: 738s 111 (100.00%) aligned concordantly 0 times 738s 0 (0.00%) aligned concordantly exactly 1 time 738s 0 (0.00%) aligned concordantly >1 times 738s ---- 738s 111 pairs aligned concordantly 0 times; of these: 738s 0 (0.00%) aligned discordantly 1 time 738s ---- 738s 111 pairs aligned 0 times concordantly or discordantly; of these: 738s 222 mates make up the pairs; of these: 738s 206 (92.79%) aligned 0 times 738s 2 (0.90%) aligned exactly 1 time 738s 14 (6.31%) aligned >1 times 738s 2 (1.77%) were unpaired; of these: 738s 1 (50.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 1 (50.00%) aligned >1 times 738s 7.59% overall alignment rate 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.2 738s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.1 738s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 11 738s Reference gaps introduced: 0 738s Read gaps introduced: 1 738s Rearrangements introduced: 0 738s Created read sampler 738s Sampling 62 reads 738s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 738s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 94 reference bases 738s *** Run 14 of 100 738s /usr/bin/bowtie2 --rdg 38.4722457854733,10.8012882522817 --rfg 10.1455351875026,13.0759867334081 --score-min L,8.27539715655556,4.10926826544469 --gbar 2 -i L,0.106848975448945 -k 2 --cp-ival 1 --local --cp-min 3 -R 4 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 738s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 738s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 738s 62 reads; of these: 738s 62 (100.00%) were unpaired; of these: 738s 62 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s Read 50 alignments... 738s /usr/bin/bowtie2 --rdg 38.4722457854733,10.8012882522817 --rfg 10.1455351875026,13.0759867334081 --score-min L,8.27539715655556,4.10926826544469 --gbar 2 -i L,0.106848975448945 -k 2 --cp-ival 1 --local --cp-min 3 -R 4 --qseq -p 2 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 0 alignments, 0 edits 738s --------------- 738s PASSED 738s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 738s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 738s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 738s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 738s 62 reads; of these: 738s 62 (100.00%) were unpaired; of these: 738s 62 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 738s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 738s /usr/bin/bowtie2 --rdg 38.4722457854733,10.8012882522817 --rfg 10.1455351875026,13.0759867334081 --score-min L,8.27539715655556,4.10926826544469 --gbar 2 -i L,0.106848975448945 -k 2 --cp-ival 1 --local --cp-min 3 -R 4 --qseq -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 738s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 738s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 738s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 738s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 738s 62 reads; of these: 738s 62 (100.00%) were unpaired; of these: 738s 62 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.1 738s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.2 738s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 9 738s Reference gaps introduced: 0 738s Read gaps introduced: 0 738s Rearrangements introduced: 0 738s Created read sampler 738s Sampling 74 reads 738s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 738s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 94 reference bases 738s *** Run 15 of 100 738s /usr/bin/bowtie2 -i C,0.915626079229739,9.0467659472372 --trim5 4 --score-min L,6.28413821857038,2.11576743230234 --rfg 15.7876899326004,10.8168859958813 --trim3 3 --cp-min 2 --cp-ival 1 --local --mp 8.55840411943586,1.01511594154167 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 738s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '1' because it was < 2 characters long 738s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '3' because it was < 2 characters long 738s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '4' because it was < 2 characters long 738s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '7' because it was < 2 characters long 738s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '8' because it was < 2 characters long 738s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '9' because it was < 2 characters long 738s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '10' because it was < 2 characters long 738s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '13' because it was < 2 characters long 738s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '15' because it was < 2 characters long 738s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '18' because it was < 2 characters long 738s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '19' because it was < 2 characters long 738s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '20' because it was < 2 characters long 738s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '24' because it was < 2 characters long 738s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '30' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '35' because it was < 2 characters long 738s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '36' because it was < 2 characters long 738s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '38' because it was < 2 characters long 738s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '46' because it was < 2 characters long 738s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '51' because it was < 2 characters long 738s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '54' because it was < 2 characters long 738s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '55' because it was < 2 characters long 738s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '67' because it was < 2 characters long 738s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '73' because it was < 2 characters long 738s 74 reads; of these: 738s 74 (100.00%) were unpaired; of these: 738s 74 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s Read 50 alignments... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 0 alignments, 0 edits 738s --------------- 738s PASSED 738s ALSO checking that bowtie2 and bowtie2-align match up 738s /usr/bin/bowtie2 -i C,0.915626079229739,9.0467659472372 --trim5 4 --score-min L,6.28413821857038,2.11576743230234 --rfg 15.7876899326004,10.8168859958813 --trim3 3 --cp-min 2 --cp-ival 1 --local --mp 8.55840411943586,1.01511594154167 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 738s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '1' because it was < 2 characters long 738s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '3' because it was < 2 characters long 738s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '4' because it was < 2 characters long 738s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '7' because it was < 2 characters long 738s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '8' because it was < 2 characters long 738s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '9' because it was < 2 characters long 738s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '10' because it was < 2 characters long 738s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '12' because it was < 2 characters long 738s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '13' because it was < 2 characters long 738s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '15' because it was < 2 characters long 738s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '18' because it was < 2 characters long 738s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '19' because it was < 2 characters long 738s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '20' because it was < 2 characters long 738s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '24' because it was < 2 characters long 738s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '30' because it was < 2 characters long 738s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '32' because it was < 2 characters long 738s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '35' because it was < 2 characters long 738s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '36' because it was < 2 characters long 738s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '38' because it was < 2 characters long 738s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '46' because it was < 2 characters long 738s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '51' because it was < 2 characters long 738s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '54' because it was < 2 characters long 738s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '55' because it was < 2 characters long 738s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '67' because it was < 2 characters long 738s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 738s Warning: skipping read '73' because it was < 2 characters long 738s 74 reads; of these: 738s 74 (100.00%) were unpaired; of these: 738s 74 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 738s Flattened IUPAC characters 738s Mutating sequence Sim.pm.2 738s Introducing 8 SNPs, 1/1 ref/read gaps, and 0 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutating sequence Sim.pm.1 738s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 738s Finished SNPs 738s Finished ref gaps 738s Finished read gaps 738s Mutated reference genome to subject genome 738s SNPs introduced: 8 738s Reference gaps introduced: 1 738s Read gaps introduced: 1 738s Rearrangements introduced: 1 738s Created read sampler 738s Sampling 35 reads 738s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 738s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 738s parsing sequence Sim.pm.1... 738s parsing sequence Sim.pm.2... 738s Parsed 94 reference bases 738s *** Run 16 of 100 738s /usr/bin/bowtie2 --mm --score-min L,3.40119621721175,9.61738884098737 --rdg 24.7046529165914 --rfg 9.77330645673492 -N 0 -L14 --cp-ival 1 --local -D 29 -M 6 --np 2 --cp-min 3 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 738s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 738s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '10' because it was < 2 characters long 738s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 738s Warning: skipping read '20' because it was < 2 characters long 738s 35 reads; of these: 738s 35 (100.00%) were unpaired; of these: 738s 35 (100.00%) aligned 0 times 738s 0 (0.00%) aligned exactly 1 time 738s 0 (0.00%) aligned >1 times 738s 0.00% overall alignment rate 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s Processing line... 738s --- Summary --- 738s Read 1 reference strings 738s Checked 0 alignments, 0 edits 738s --------------- 738s PASSED 738s ALSO checking that bowtie2 and bowtie2-align match up 738s /usr/bin/bowtie2 --mm --score-min L,3.40119621721175,9.61738884098737 --rdg 24.7046529165914 --rfg 9.77330645673492 -N 0 -L14 --cp-ival 1 --local -D 29 -M 6 --np 2 --cp-min 3 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '10' because it was < 2 characters long 739s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '20' because it was < 2 characters long 739s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 739s /usr/bin/bowtie2 --mm --score-min L,3.40119621721175,9.61738884098737 --rdg 24.7046529165914 --rfg 9.77330645673492 -N 0 -L14 --cp-ival 1 --local -D 29 -M 6 --np 2 --cp-min 3 -q -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 739s 35 reads; of these: 739s 35 (100.00%) were unpaired; of these: 739s 35 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '10' because it was < 2 characters long 739s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '20' because it was < 2 characters long 739s 35 reads; of these: 739s 35 (100.00%) were unpaired; of these: 739s 35 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 5 SNPs, 2/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 9 739s Reference gaps introduced: 2 739s Read gaps introduced: 0 739s Rearrangements introduced: 0 739s Created read sampler 739s Sampling 95 reads 739s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 739s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 94 reference bases 739s *** Run 17 of 100 739s /usr/bin/bowtie2 --cp-min 4 -R 4 --cp-ival 1 --local --trim3 4 --rdg 49.1299996529939,12.4405236623457 --score-min L,4.61890083533086,5.52746695086113 --mm --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 739s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 739s 95 reads; of these: 739s 95 (100.00%) were unpaired; of these: 739s 95 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Read 50 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 0 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2-align match up 739s /usr/bin/bowtie2 --cp-min 4 -R 4 --cp-ival 1 --local --trim3 4 --rdg 49.1299996529939,12.4405236623457 --score-min L,4.61890083533086,5.52746695086113 --mm --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 739s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 739s 95 reads; of these: 739s 95 (100.00%) were unpaired; of these: 739s 95 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 739s /usr/bin/bowtie2 --cp-min 4 -R 4 --cp-ival 1 --local --trim3 4 --rdg 49.1299996529939,12.4405236623457 --score-min L,4.61890083533086,5.52746695086113 --mm --qseq -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 739s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 739s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 739s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 739s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 739s 95 reads; of these: 739s 95 (100.00%) were unpaired; of these: 739s 95 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.1 739s Introducing 4 SNPs, 0/1 ref/read gaps, and 3 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.2 739s Introducing 9 SNPs, 0/3 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 13 739s Reference gaps introduced: 0 739s Read gaps introduced: 4 739s Rearrangements introduced: 3 739s Created read sampler 739s Sampling 159 reads 739s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 739s *** Run 18 of 100 739s /usr/bin/bowtie2 --mm --gbar 1 --score-min L,7.34523979404261,4.93850167178206 --rdg 25.3006367318119,2.68153420180567 --cp-ival 2 --local --nofw --mp 5.17103994057439,3.50247135838031 -i C,2.27931274973861 --trim5 8 --cp-min 3 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 739s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 94 reference bases 739s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '2' because it was < 2 characters long 739s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '14' because it was < 2 characters long 739s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '15' because it was < 2 characters long 739s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '19' because it was < 2 characters long 739s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '20' because it was < 2 characters long 739s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '21' because it was < 2 characters long 739s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '24' because it was < 2 characters long 739s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '25' because it was < 2 characters long 739s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '26' because it was < 2 characters long 739s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '29' because it was < 2 characters long 739s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '32' because it was < 2 characters long 739s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '36' because it was < 2 characters long 739s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '40' because it was < 2 characters long 739s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '45' because it was < 2 characters long 739s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '47' because it was < 2 characters long 739s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '64' because it was < 2 characters long 739s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '69' because it was < 2 characters long 739s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '70' because it was < 2 characters long 739s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '74' because it was < 2 characters long 739s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '77' because it was < 2 characters long 739s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '79' because it was < 2 characters long 739s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '89' because it was < 2 characters long 739s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '99' because it was < 2 characters long 739s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '106' because it was < 2 characters long 739s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '110' because it was < 2 characters long 739s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '112' because it was < 2 characters long 739s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '116' because it was < 2 characters long 739s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '118' because it was < 2 characters long 739s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '128' because it was < 2 characters long 739s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '134' because it was < 2 characters long 739s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '135' because it was < 2 characters long 739s Warning: skipping mate #1 of read '142' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '142' because it was < 2 characters long 739s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '143' because it was < 2 characters long 739s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '144' because it was < 2 characters long 739s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '151' because it was < 2 characters long 739s Warning: skipping mate #1 of read '158' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '158' because it was < 2 characters long 739s Read 50 alignments... 739s Read 100 alignments... 739s 159 reads; of these: 739s 134 (84.28%) were paired; of these: 739s 134 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 134 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 134 pairs aligned 0 times concordantly or discordantly; of these: 739s 268 mates make up the pairs; of these: 739s 268 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 25 (15.72%) were unpaired; of these: 739s 25 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Read 150 alignments... 739s Read 200 alignments... 739s Read 250 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s /usr/bin/bowtie2 --mm --gbar 1 --score-min L,7.34523979404261,4.93850167178206 --rdg 25.3006367318119,2.68153420180567 --cp-ival 2 --local --nofw --mp 5.17103994057439,3.50247135838031 -i C,2.27931274973861 --trim5 8 --cp-min 3 -f -p 2 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 739s Read 1 reference strings 739s Checked 0 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 739s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '2' because it was < 2 characters long 739s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '14' because it was < 2 characters long 739s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '15' because it was < 2 characters long 739s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '19' because it was < 2 characters long 739s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '20' because it was < 2 characters long 739s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '21' because it was < 2 characters long 739s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '24' because it was < 2 characters long 739s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '25' because it was < 2 characters long 739s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '26' because it was < 2 characters long 739s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '29' because it was < 2 characters long 739s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '32' because it was < 2 characters long 739s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '36' because it was < 2 characters long 739s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '40' because it was < 2 characters long 739s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '45' because it was < 2 characters long 739s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '47' because it was < 2 characters long 739s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '64' because it was < 2 characters long 739s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '69' because it was < 2 characters long 739s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '70' because it was < 2 characters long 739s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '74' because it was < 2 characters long 739s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '77' because it was < 2 characters long 739s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '79' because it was < 2 characters long 739s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '89' because it was < 2 characters long 739s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '99' because it was < 2 characters long 739s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '106' because it was < 2 characters long 739s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '110' because it was < 2 characters long 739s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '112' because it was < 2 characters long 739s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '116' because it was < 2 characters long 739s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '118' because it was < 2 characters long 739s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '128' because it was < 2 characters long 739s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '134' because it was < 2 characters long 739s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '135' because it was < 2 characters long 739s Warning: skipping mate #1 of read '142' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '142' because it was < 2 characters long 739s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '143' because it was < 2 characters long 739s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '144' because it was < 2 characters long 739s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '151' because it was < 2 characters long 739s Warning: skipping mate #1 of read '158' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '158' because it was < 2 characters long 739s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 739s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 739s 159 reads; of these: 739s 134 (84.28%) were paired; of these: 739s 134 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 134 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 134 pairs aligned 0 times concordantly or discordantly; of these: 739s 268 mates make up the pairs; of these: 739s 268 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 25 (15.72%) were unpaired; of these: 739s 25 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 8 739s Reference gaps introduced: 1 739s Read gaps introduced: 0 739s Rearrangements introduced: 1 739s Created read sampler 739s Sampling 128 reads 739s *** Run 19 of 100 739s /usr/bin/bowtie2 --score-min L,6.45195245948432,8.25035200793292 --trim5 4 -M 2 --ma 4.60891762085166 --cp-ival 1 -D 7 --n-ceil 0.44617160336328,0.0474341921656888 --cp-min 11 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 739s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 739s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 94 reference bases 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 739s Warning: skipping mate #1 of read '1' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '1' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 739s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '19' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 739s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '32' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 739s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '52' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 739s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '59' because it was < 2 characters long 739s Warning: skipping mate #2 of read '59' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 739s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '61' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 739s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '64' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 739s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '89' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 739s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '99' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 739s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '101' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 739s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '110' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 739s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '127' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 739s Read 50 alignments... 739s 128 reads; of these: 739s 116 (90.62%) were paired; of these: 739s 116 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 116 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 116 pairs aligned 0 times concordantly or discordantly; of these: 739s 232 mates make up the pairs; of these: 739s 215 (92.67%) aligned 0 times 739s 4 (1.72%) aligned exactly 1 time 739s 13 (5.60%) aligned >1 times 739s 12 (9.38%) were unpaired; of these: 739s 10 (83.33%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 2 (16.67%) aligned >1 times 739s 7.79% overall alignment rate 739s Read 100 alignments... 739s Read 150 alignments... 739s Read 200 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TCAACACC 739s TCAACACC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s AC 739s AC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GCGTCAACACCTG 739s GCGTCAACACCTG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GTCA 739s GTCA 739s Processing line... 739s GTCA 739s GTCA 739s Processing line... 739s Processing line... 739s CTG 739s CTG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s ACAC 739s ACAC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s ATG 739s ATG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TCAA 739s TCAA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CT 739s CT 739s Processing line... 739s ATAACACAT 739s ATAACACAT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CAT 739s CAT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TGC 739s TGC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s AA 739s AA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GGCGTCA 739s GGCGTCA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GAAA 739s GAAA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GAAC 739s GAAC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s ATGGATTCAA 739s ATGGATTCAA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TCAA 739s TCAA 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 19 alignments, 0 edits 739s --------------- 739s PASSED 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.1 739s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.2 739s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 3 739s Reference gaps introduced: 0 739s *** Run 20 of 100 739s /usr/bin/bowtie2 --local --cp-ival 2 --nofw --mp 7.21923760587126,3.60752439109589 --gbar 7 --score-min L,9.77542700381544,6.77872663791839 --rdg 45.932199399563 --cp-min 2 --np 2 -k 4 --trim5 8 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 739s Read gaps introduced: 0 739s Rearrangements introduced: 0 739s Created read sampler 739s Sampling 48 reads 739s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 739s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 94 reference bases 739s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '2' because it was < 2 characters long 739s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '4' because it was < 2 characters long 739s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '5' because it was < 2 characters long 739s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '13' because it was < 2 characters long 739s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '14' because it was < 2 characters long 739s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '20' because it was < 2 characters long 739s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '24' because it was < 2 characters long 739s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '25' because it was < 2 characters long 739s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '28' because it was < 2 characters long 739s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '31' because it was < 2 characters long 739s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '35' because it was < 2 characters long 739s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '36' because it was < 2 characters long 739s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '42' because it was < 2 characters long 739s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '45' because it was < 2 characters long 739s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '46' because it was < 2 characters long 739s 48 reads; of these: 739s 48 (100.00%) were unpaired; of these: 739s 48 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Read 50 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 0 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2-align match up 739s /usr/bin/bowtie2 --local --cp-ival 2 --nofw --mp 7.21923760587126,3.60752439109589 --gbar 7 --score-min L,9.77542700381544,6.77872663791839 --rdg 45.932199399563 --cp-min 2 --np 2 -k 4 --trim5 8 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 739s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '2' because it was < 2 characters long 739s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '4' because it was < 2 characters long 739s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '5' because it was < 2 characters long 739s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '13' because it was < 2 characters long 739s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '14' because it was < 2 characters long 739s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '20' because it was < 2 characters long 739s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '24' because it was < 2 characters long 739s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '25' because it was < 2 characters long 739s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '28' because it was < 2 characters long 739s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '31' because it was < 2 characters long 739s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '35' because it was < 2 characters long 739s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '36' because it was < 2 characters long 739s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '42' because it was < 2 characters long 739s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '45' because it was < 2 characters long 739s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '46' because it was < 2 characters long 739s 48 reads; of these: 739s 48 (100.00%) were unpaired; of these: 739s 48 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 739s /usr/bin/bowtie2 --local --cp-ival 2 --nofw --mp 7.21923760587126,3.60752439109589 --gbar 7 --score-min L,9.77542700381544,6.77872663791839 --rdg 45.932199399563 --cp-min 2 --np 2 -k 4 --trim5 8 -r -p 3 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 739s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 739s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '2' because it was < 2 characters long 739s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '4' because it was < 2 characters long 739s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '5' because it was < 2 characters long 739s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '13' because it was < 2 characters long 739s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '14' because it was < 2 characters long 739s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '20' because it was < 2 characters long 739s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '24' because it was < 2 characters long 739s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '25' because it was < 2 characters long 739s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '28' because it was < 2 characters long 739s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '31' because it was < 2 characters long 739s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '35' because it was < 2 characters long 739s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '36' because it was < 2 characters long 739s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '42' because it was < 2 characters long 739s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '45' because it was < 2 characters long 739s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '46' because it was < 2 characters long 739s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 739s 48 reads; of these: 739s 48 (100.00%) were unpaired; of these: 739s 48 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 739s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 739s /usr/bin/bowtie2 --local --cp-ival 2 --nofw --mp 7.21923760587126,3.60752439109589 --gbar 7 --score-min L,9.77542700381544,6.77872663791839 --rdg 45.932199399563 --cp-min 2 --np 2 -k 4 --trim5 8 -r -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 739s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 739s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '2' because it was < 2 characters long 739s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '4' because it was < 2 characters long 739s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '5' because it was < 2 characters long 739s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '13' because it was < 2 characters long 739s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '14' because it was < 2 characters long 739s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '20' because it was < 2 characters long 739s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '24' because it was < 2 characters long 739s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '25' because it was < 2 characters long 739s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '28' because it was < 2 characters long 739s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '31' because it was < 2 characters long 739s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '35' because it was < 2 characters long 739s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '36' because it was < 2 characters long 739s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 739s Warning: skipping read '42' because it was < 2 characters long 739s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '45' because it was < 2 characters long 739s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 739s Warning: skipping read '46' because it was < 2 characters long 739s 48 reads; of these: 739s 48 (100.00%) were unpaired; of these: 739s 48 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 10 739s Reference gaps introduced: 0 739s Read gaps introduced: 0 739s Rearrangements introduced: 0 739s Created read sampler 739s Sampling 82 reads 739s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 739s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 94 reference bases 739s *** Run 21 of 100 739s /usr/bin/bowtie2 --cp-min 2 --np 5 -M 3 --n-ceil 1.37665904034675,0.39251725439167 --cp-ival 1 --nofw -N 0 -L30 --mp 3.63635517614437,2.6384148184514 --gbar 2 --score-min L,8.40271505631077,5.66764044843122 --rfg 12.1090507443386 --mm -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 739s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 739s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #1 of read '7' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 739s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '33' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 739s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 739s Warning: skipping mate #2 of read '61' because it was < 2 characters long 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 739s Read 50 alignments... 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 739s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 739s Read 100 alignments... 739s 82 reads; of these: 739s 82 (100.00%) were paired; of these: 739s 82 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 82 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 82 pairs aligned 0 times concordantly or discordantly; of these: 739s 164 mates make up the pairs; of these: 739s 156 (95.12%) aligned 0 times 739s 1 (0.61%) aligned exactly 1 time 739s 7 (4.27%) aligned >1 times 739s 4.88% overall alignment rate 739s Read 150 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s AA 739s AA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CGA 739s CGA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s AT 739s AT 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CCG 739s CCG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s CA 739s CA 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s GAACATGGATTCAATCATAACACATT 739s GAACATGGATTCAATCATAACACATT 739s Processing line... 739s Processing line... 739s TG 739s TG 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s TC 739s TC 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 8 alignments, 0 edits 739s --------------- 739s PASSED 739s Flattened IUPAC characters 739s Mutating sequence Sim.pm.2 739s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutating sequence Sim.pm.1 739s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 739s Finished SNPs 739s Finished ref gaps 739s Finished read gaps 739s Mutated reference genome to subject genome 739s SNPs introduced: 9 739s Reference gaps introduced: 1 739s Read gaps introduced: 1 739s Rearrangements introduced: 0 739s Created read sampler 739s Sampling 80 reads 739s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 739s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 739s parsing sequence Sim.pm.1... 739s parsing sequence Sim.pm.2... 739s Parsed 94 reference bases 739s *** Run 22 of 100 739s /usr/bin/bowtie2 --mm --rfg 33.6229385114041,15.6613879703069 --score-min L,5.10524548075435,9.2242597299917 -N 1 -L30 --nofw --cp-ival 1 -D 24 --n-ceil 0.964264152786906,0.718524503323521 --local --trim5 5 -i S,1.46594156911831 -R 2 --cp-min 6 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 739s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '5' because it was < 2 characters long 739s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '6' because it was < 2 characters long 739s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '34' because it was < 2 characters long 739s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '36' because it was < 2 characters long 739s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '40' because it was < 2 characters long 739s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '44' because it was < 2 characters long 739s Read 50 alignments... 739s Read 100 alignments... 739s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '78' because it was < 2 characters long 739s 80 reads; of these: 739s 68 (85.00%) were paired; of these: 739s 68 (100.00%) aligned concordantly 0 times 739s 0 (0.00%) aligned concordantly exactly 1 time 739s 0 (0.00%) aligned concordantly >1 times 739s ---- 739s 68 pairs aligned concordantly 0 times; of these: 739s 0 (0.00%) aligned discordantly 1 time 739s ---- 739s 68 pairs aligned 0 times concordantly or discordantly; of these: 739s 136 mates make up the pairs; of these: 739s 136 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 12 (15.00%) were unpaired; of these: 739s 12 (100.00%) aligned 0 times 739s 0 (0.00%) aligned exactly 1 time 739s 0 (0.00%) aligned >1 times 739s 0.00% overall alignment rate 739s Read 150 alignments... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s Processing line... 739s --- Summary --- 739s Read 1 reference strings 739s Checked 0 alignments, 0 edits 739s --------------- 739s PASSED 739s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 739s /usr/bin/bowtie2 --mm --rfg 33.6229385114041,15.6613879703069 --score-min L,5.10524548075435,9.2242597299917 -N 1 -L30 --nofw --cp-ival 1 -D 24 --n-ceil 0.964264152786906,0.718524503323521 --local --trim5 5 -i S,1.46594156911831 -R 2 --cp-min 6 -r -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 739s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '5' because it was < 2 characters long 739s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '6' because it was < 2 characters long 739s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 739s Warning: skipping read '34' because it was < 2 characters long 739s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '36' because it was < 2 characters long 739s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '40' because it was < 2 characters long 739s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '44' because it was < 2 characters long 739s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (1) 739s Warning: skipping mate #1 of read '78' because it was < 2 characters long 740s 80 reads; of these: 740s 68 (85.00%) were paired; of these: 740s 68 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 68 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 68 pairs aligned 0 times concordantly or discordantly; of these: 740s 136 mates make up the pairs; of these: 740s 136 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 12 (15.00%) were unpaired; of these: 740s 12 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 0.00% overall alignment rate 740s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.1 740s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.2 740s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 0 740s Reference gaps introduced: 0 740s Read gaps introduced: 0 740s Rearrangements introduced: 0 740s Created read sampler 740s Sampling 64 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s *** Run 23 of 100 740s /usr/bin/bowtie2 --cp-ival 1 --cp-min 7 --np 3 --rdg 3.9790394423615,7.99730358262118 --rfg 24.8204394680156,19.8781654581633 --score-min L,5.88010257054526,8.75040065068009 -k 2 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 740s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 740s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '31' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 740s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '38' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 740s 64 reads; of these: 740s 64 (100.00%) were unpaired; of these: 740s 54 (84.38%) aligned 0 times 740s 5 (7.81%) aligned exactly 1 time 740s 5 (7.81%) aligned >1 times 740s 15.62% overall alignment rate 740s Read 50 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGC 740s GGC 740s Processing line... 740s GGC 740s GGC 740s Processing line... 740s Processing line... 740s CATGGATTCAATC 740s CATGGATTCAATC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTGGCGTCAACAC 740s TTGGCGTCAACAC 740s Processing line... 740s TTGGCGTCAACAC 740s TTGGCGTCAACAC 740s Processing line... 740s CGAA 740s CGAA 740s Processing line... 740s CGAA 740s CGAA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CCCGAA 740s CCCGAA 740s Processing line... 740s CCCGAA 740s CCCGAA 740s Processing line... 740s CGTCAACAC 740s CGTCAACAC 740s Processing line... 740s CGTCAACAC 740s CGTCAACAC 740s Processing line... 740s TAAC 740s TAAC 740s Processing line... 740s Processing line... 740s Processing line... 740s CAATCAT 740s CAATCAT 740s Processing line... 740s Processing line... 740s Processing line... 740s AACATGGATTCAATCAT 740s AACATGGATTCAATCAT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CATGA 740s CATGA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 15 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 2 SNPs, 0/2 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 5 740s Reference gaps introduced: 0 740s Read gaps introduced: 2 740s Rearrangements introduced: 0 740s Created read sampler 740s Sampling 105 reads 740s *** Run 24 of 100 740s /usr/bin/bowtie2 --rfg 48.1998436846709 --rdg 2.21774810250317,10.4258762920273 --score-min L,8.68110695988596,9.50547024559461 -R 2 --trim3 4 --mp 9.86101832528904,1.45528807104541 --cp-ival 3 --local --n-ceil 0.02328374328982,0.727146882939844 --cp-min 3 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '1' because it was < 2 characters long 740s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '2' because it was < 2 characters long 740s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '10' because it was < 2 characters long 740s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '12' because it was < 2 characters long 740s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '14' because it was < 2 characters long 740s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '17' because it was < 2 characters long 740s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '18' because it was < 2 characters long 740s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '25' because it was < 2 characters long 740s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '27' because it was < 2 characters long 740s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '31' because it was < 2 characters long 740s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '38' because it was < 2 characters long 740s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '55' because it was < 2 characters long 740s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '58' because it was < 2 characters long 740s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '64' because it was < 2 characters long 740s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '83' because it was < 2 characters long 740s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '94' because it was < 2 characters long 740s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '96' because it was < 2 characters long 740s Warning: skipping read '99' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '99' because it was < 2 characters long 740s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '101' because it was < 2 characters long 740s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '103' because it was < 2 characters long 740s 105 reads; of these: 740s 105 (100.00%) were unpaired; of these: 740s 105 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 0.00% overall alignment rate 740s Read 50 alignments... 740s Read 100 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 0 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 11 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 11 740s Reference gaps introduced: 0 740s Read gaps introduced: 0 740s Rearrangements introduced: 1 740s Created read sampler 740s Sampling 81 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s *** Run 25 of 100 740s /usr/bin/bowtie2 --cp-ival 2 --local --n-ceil 1.0067627888987,0.471303703757383 --trim3 1 --score-min L,6.64997823641084,6.69859324320239 --gbar 4 --cp-min 2 --norc --np 3 --trim5 9 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '2' because it was < 2 characters long 740s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '6' because it was < 2 characters long 740s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read '7' because it was < 2 characters long 740s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '8' because it was < 2 characters long 740s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '11' because it was < 2 characters long 740s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '14' because it was < 2 characters long 740s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '18' because it was < 2 characters long 740s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '19' because it was < 2 characters long 740s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read '21' because it was < 2 characters long 740s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '29' because it was < 2 characters long 740s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read '33' because it was < 2 characters long 740s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '40' because it was < 2 characters long 740s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '41' because it was < 2 characters long 740s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '45' because it was < 2 characters long 740s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '54' because it was < 2 characters long 740s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '56' because it was < 2 characters long 740s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '60' because it was < 2 characters long 740s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '62' because it was < 2 characters long 740s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '68' because it was < 2 characters long 740s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '74' because it was < 2 characters long 740s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read '78' because it was < 2 characters long 740s Read 50 alignments... 740s 81 reads; of these: 740s 63 (77.78%) were paired; of these: 740s 63 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 63 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 63 pairs aligned 0 times concordantly or discordantly; of these: 740s 126 mates make up the pairs; of these: 740s 126 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 18 (22.22%) were unpaired; of these: 740s 18 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 0.00% overall alignment rate 740s Read 100 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 0 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 6 740s Reference gaps introduced: 0 740s Read gaps introduced: 0 740s Rearrangements introduced: 2 740s Created read sampler 740s Sampling 104 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s *** Run 26 of 100 740s /usr/bin/bowtie2 -M 10 --trim5 2 --cp-min 3 --score-min L,1.81778028118951,3.59097071421915 --rfg 39.9058478758657,9.84944328861436 --cp-ival 1 --n-ceil 0.153899356295096,1.00224657109518 --local --trim3 5 -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta 740s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 740s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '6' because it was < 2 characters long 740s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '8' because it was < 2 characters long 740s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '9' because it was < 2 characters long 740s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '18' because it was < 2 characters long 740s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '24' because it was < 2 characters long 740s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '27' because it was < 2 characters long 740s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '33' because it was < 2 characters long 740s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '36' because it was < 2 characters long 740s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '47' because it was < 2 characters long 740s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '48' because it was < 2 characters long 740s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '53' because it was < 2 characters long 740s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '55' because it was < 2 characters long 740s Warning: skipping read '61' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '61' because it was < 2 characters long 740s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '63' because it was < 2 characters long 740s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '64' because it was < 2 characters long 740s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '69' because it was < 2 characters long 740s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '70' because it was < 2 characters long 740s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '71' because it was < 2 characters long 740s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '79' because it was < 2 characters long 740s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '84' because it was < 2 characters long 740s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '90' because it was < 2 characters long 740s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '95' because it was < 2 characters long 740s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '96' because it was < 2 characters long 740s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '97' because it was < 2 characters long 740s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '100' because it was < 2 characters long 740s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '103' because it was < 2 characters long 740s 104 reads; of these: 740s 104 (100.00%) were unpaired; of these: 740s 104 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 0.00% overall alignment rate 740s Read 50 alignments... 740s Read 100 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 0 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.1 740s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.2 740s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 4 740s Reference gaps introduced: 0 740s Read gaps introduced: 0 740s Rearrangements introduced: 2 740s Created read sampler 740s Sampling 38 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s *** Run 27 of 100 740s /usr/bin/bowtie2 -a --score-min L,6.58075748075004,2.96072814784101 --rdg 30.3236413796011 --cp-min 6 --cp-ival 3 --mp 8.28498533751059,3.70649127757724 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 740s 38 reads; of these: 740s 38 (100.00%) were unpaired; of these: 740s 24 (63.16%) aligned 0 times 740s 2 (5.26%) aligned exactly 1 time 740s 12 (31.58%) aligned >1 times 740s 36.84% overall alignment rate 740s Read 50 alignments... 740s Processing line... 740s Processing line... 740s /usr/bin/bowtie2 -a --score-min L,6.58075748075004,2.96072814784101 --rdg 30.3236413796011 --cp-min 6 --cp-ival 3 --mp 8.28498533751059,3.70649127757724 --qseq -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GCGTCAAC 740s GCGTCAAC 740s Processing line... 740s GCGTCAAC 740s GCGTCAAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CAATC 740s CAATC 740s Processing line... 740s TGG 740s TGG 740s Processing line... 740s TGG 740s TGG 740s Processing line... 740s TGG 740s TGG 740s Processing line... 740s Processing line... 740s TG 740s TG 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s TG 740s TG 740s Processing line... 740s CA 740s CA 740s Processing line... 740s TG 740s TG 740s Processing line... 740s CA 740s CA 740s Processing line... 740s TG 740s TG 740s Processing line... 740s TG 740s TG 740s Processing line... 740s CA 740s CA 740s Processing line... 740s TG 740s TG 740s Processing line... 740s TG 740s TG 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTGGCG 740s TTGGCG 740s Processing line... 740s TTGGCG 740s TTGGCG 740s Processing line... 740s ACA 740s ACA 740s Processing line... 740s ACA 740s ACA 740s Processing line... 740s ACA 740s ACA 740s Processing line... 740s ACA 740s ACA 740s Processing line... 740s ACA 740s ACA 740s Processing line... 740s CGA 740s CGA 740s Processing line... 740s CGA 740s CGA 740s Processing line... 740s CC 740s CC 740s Processing line... 740s GG 740s GG 740s Processing line... 740s CC 740s CC 740s Processing line... 740s CC 740s CC 740s Processing line... 740s GG 740s GG 740s Processing line... 740s CC 740s CC 740s Processing line... 740s CC 740s CC 740s Processing line... 740s CC 740s CC 740s Processing line... 740s GG 740s GG 740s Processing line... 740s Processing line... 740s AA 740s AA 740s Processing line... 740s AA 740s AA 740s Processing line... 740s AA 740s AA 740s Processing line... 740s TT 740s TT 740s Processing line... 740s TT 740s TT 740s Processing line... 740s TT 740s TT 740s Processing line... 740s TT 740s TT 740s Processing line... 740s AA 740s AA 740s Processing line... 740s AA 740s AA 740s Processing line... 740s AA 740s AA 740s Processing line... 740s AA 740s AA 740s Processing line... 740s AA 740s AA 740s Processing line... 740s AA 740s AA 740s Processing line... 740s TT 740s TT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TGA 740s TGA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TGC 740s TGC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTGG 740s TTGG 740s Processing line... 740s TTGG 740s TTGG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTGGCGTC 740s TTGGCGTC 740s Processing line... 740s TTGGCGTC 740s TTGGCGTC 740s Processing line... 740s Processing line... 740s Processing line... 740s AAC 740s AAC 740s Processing line... 740s AAC 740s AAC 740s Processing line... 740s AAC 740s AAC 740s Processing line... 740s AAC 740s AAC 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 70 alignments, 0 edits 740s --------------- 740s PASSED 740s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 740s 38 reads; of these: 740s 38 (100.00%) were unpaired; of these: 740s 24 (63.16%) aligned 0 times 740s 2 (5.26%) aligned exactly 1 time 740s 12 (31.58%) aligned >1 times 740s 36.84% overall alignment rate 740s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 9 740s Reference gaps introduced: 1 740s Read gaps introduced: 1 740s Rearrangements introduced: 0 740s Created read sampler 740s Sampling 204 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s *** Run 28 of 100 740s /usr/bin/bowtie2 --nofw --cp-ival 1 --cp-min 2 --trim3 0 --rdg 27.5355651264652 --score-min L,7.93354813724365,1.8598962910898 --np 1 -a --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 740s Read 50 alignments... 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 740s Read 100 alignments... 740s Read 150 alignments... 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_137_137_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 740s Read 200 alignments... 740s Read 250 alignments... 740s Read 300 alignments... 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_152_152_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_178_178_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_178_178_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_181_181_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_181_181_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_185_185_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_185_185_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_187_187_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_187_187_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_188_188_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_188_188_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_189_189_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_189_189_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_190_190_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_190_190_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_191_191_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_191_191_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_192_192_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_192_192_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_193_193_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_193_193_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_194_194_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_194_194_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_195_195_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_195_195_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_196_196_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_196_196_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_197_197_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_197_197_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_198_198_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_198_198_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_199_199_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_199_199_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_200_200_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_200_200_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_201_201_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_201_201_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_202_202_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_202_202_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_203_203_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_203_203_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_204_204_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_204_204_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_204_204_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_204_204_1/1' because it was < 2 characters long 740s Read 350 alignments... 740s 204 reads; of these: 740s 204 (100.00%) were paired; of these: 740s 203 (99.51%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 1 (0.49%) aligned concordantly >1 times 740s ---- 740s 203 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 203 pairs aligned 0 times concordantly or discordantly; of these: 740s 406 mates make up the pairs; of these: 740s 376 (92.61%) aligned 0 times 740s 3 (0.74%) aligned exactly 1 time 740s 27 (6.65%) aligned >1 times 740s 7.84% overall alignment rate 740s Read 400 alignments... 740s Read 450 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CCCGA 740s CCCGA 740s Processing line... 740s GTC 740s GTC 740s Processing line... 740s CCCGA 740s CCCGA 740s Processing line... 740s GTC 740s GTC 740s Processing line... 740s CCCGA 740s CCCGA 740s Processing line... 740s GTC 740s GTC 740s Processing line... 740s GCGTCAACAC 740s GCGTCAACAC 740s Processing line... 740s GCGTCAACAC 740s GCGTCAACAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s CA 740s CA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTG 740s TTG 740s Processing line... 740s TTG 740s TTG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TG 740s TG 740s Processing line... 740s TG 740s TG 740s Processing line... 740s TG 740s TG 740s Processing line... 740s TG 740s TG 740s Processing line... 740s TG 740s TG 740s Processing line... 740s TG 740s TG 740s Processing line... 740s TG 740s TG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GGCGT 740s GGCGT 740s Processing line... 740s GGCGT 740s GGCGT 740s Processing line... 740s Processing line... 740s GTCAACAC 740s GTCAACAC 740s Processing line... 740s GTCAACAC 740s GTCAACAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TGA 740s TGA 740s Processing line... 740s Processing line... 740s CT 740s CT 740s Processing line... 740s CT 740s CT 740s Processing line... 740s CT 740s CT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s AC 740s AC 740s Processing line... 740s AC 740s AC 740s Processing line... 740s AC 740s AC 740s Processing line... 740s AC 740s AC 740s Processing line... 740s AC 740s AC 740s Processing line... 740s AC 740s AC 740s Processing line... 740s AC 740s AC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TA 740s TA 740s Processing line... 740s TA 740s TA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CATA 740s CATA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CAC 740s CAC 740s Processing line... 740s CAC 740s CAC 740s Processing line... 740s CAC 740s CAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CAT 740s CAT 740s Processing line... 740s CAT 740s CAT 740s Processing line... 740s CAT 740s CAT 740s Processing line... 740s CAT 740s CAT 740s Processing line... 740s Processing line... 740s GTCAAC 740s GTCAAC 740s Processing line... 740s GTCAAC 740s GTCAAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s AACAC 740s AACAC 740s Processing line... 740s AACAC 740s AACAC 740s Processing line... 740s AACAC 740s AACAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TGGCGTCAACACC 740s TGGCGTCAACACC 740s Processing line... 740s TGGCGTCAACACC 740s TGGCGTCAACACC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s AT 740s AT 740s Processing line... 740s AT 740s AT 740s Processing line... 740s AT 740s AT 740s Processing line... 740s AT 740s AT 740s Processing line... 740s AT 740s AT 740s Processing line... 740s AT 740s AT 740s Processing line... 740s AT 740s AT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GCG 740s GCG 740s Processing line... 740s GCG 740s GCG 740s Processing line... 740s Processing line... 740s GCGTCAA 740s GCGTCAA 740s Processing line... 740s GCGTCAA 740s GCGTCAA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CGTCAACACCT 740s CGTCAACACCT 740s Processing line... 740s CGTCAACACCT 740s CGTCAACACCT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CCG 740s CCG 740s Processing line... 740s CCG 740s CCG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GA 740s GA 740s Processing line... 740s GA 740s GA 740s Processing line... 740s GA 740s GA 740s Processing line... 740s GA 740s GA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s ATG 740s ATG 740s Processing line... 740s ATG 740s ATG 740s Processing line... 740s ATG 740s ATG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTGGCGTCAACAC 740s TTGGCGTCAACAC 740s Processing line... 740s TTGGCGTCAACAC 740s TTGGCGTCAACAC 740s Processing line... 740s Processing line... 740s GT 740s GT 740s Processing line... 740s GT 740s GT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TTGGCG 740s TTGGCG 740s Processing line... 740s TTGGCG 740s TTGGCG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s GC 740s GC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TGA 740s TGA 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 100 alignments, 0 edits 740s --------------- 740s PASSED 740s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 740s /usr/bin/bowtie2 --nofw --cp-ival 1 --cp-min 2 --trim3 0 --rdg 27.5355651264652 --score-min L,7.93354813724365,1.8598962910898 --np 1 -a --qseq -p 3 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_137_137_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_152_152_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_152_152_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_169_169_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_176_176_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_178_178_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_178_178_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_181_181_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_181_181_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_182_182_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_183_183_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_184_184_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_185_185_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_185_185_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_186_186_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_187_187_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_187_187_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_188_188_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_188_188_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_189_189_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_189_189_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_190_190_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_190_190_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_191_191_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_191_191_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_192_192_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_192_192_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_193_193_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_193_193_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_194_194_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_194_194_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_195_195_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_195_195_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_196_196_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_196_196_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_197_197_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_197_197_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_198_198_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_198_198_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_199_199_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_199_199_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_200_200_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_200_200_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_201_201_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_201_201_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_202_202_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_202_202_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_203_203_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_203_203_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_204_204_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_204_204_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_204_204_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_204_204_1/1' because it was < 2 characters long 740s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 740s 204 reads; of these: 740s 204 (100.00%) were paired; of these: 740s 203 (99.51%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 1 (0.49%) aligned concordantly >1 times 740s ---- 740s 203 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 203 pairs aligned 0 times concordantly or discordantly; of these: 740s 406 mates make up the pairs; of these: 740s 376 (92.61%) aligned 0 times 740s 3 (0.74%) aligned exactly 1 time 740s 27 (6.65%) aligned >1 times 740s 7.84% overall alignment rate 740s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 740s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.1 740s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.2 740s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 3 740s Reference gaps introduced: 0 740s Read gaps introduced: 0 740s Rearrangements introduced: 1 740s Created read sampler 740s Sampling 2 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s *** Run 29 of 100 740s /usr/bin/bowtie2 --trim3 6 --cp-min 4 --cp-ival 3 --local --mp 8.88359697633691,8.68288662240159 --score-min L,2.15726962702718,8.28168025656735 --rfg 18.5705033743255,19.0689949355389 --rdg 16.5720257361523 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 740s 2 reads; of these: 740s 2 (100.00%) were unpaired; of these: 740s 2 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 0.00% overall alignment rate 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 0 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.1 740s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.2 740s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 6 740s Reference gaps introduced: 0 740s Read gaps introduced: 0 740s Rearrangements introduced: 1 740s Created read sampler 740s Sampling 115 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s *** Run 30 of 100 740s /usr/bin/bowtie2 --score-min L,2.2951057679411,1.14437962056709 --rdg 22.2071266633485,9.7703811575111 --trim3 4 --local --cp-ival 4 -D 27 --mp 8.89610512329682,7.22939688363054 --trim5 4 --norc --cp-min 3 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 740s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '0' because it was < 2 characters long 740s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '2' because it was < 2 characters long 740s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '3' because it was < 2 characters long 740s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '4' because it was < 2 characters long 740s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '12' because it was < 2 characters long 740s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '13' because it was < 2 characters long 740s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '17' because it was < 2 characters long 740s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '19' because it was < 2 characters long 740s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '20' because it was < 2 characters long 740s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '26' because it was < 2 characters long 740s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '32' because it was < 2 characters long 740s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '36' because it was < 2 characters long 740s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '39' because it was < 2 characters long 740s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '40' because it was < 2 characters long 740s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '43' because it was < 2 characters long 740s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '44' because it was < 2 characters long 740s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '54' because it was < 2 characters long 740s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '57' because it was < 2 characters long 740s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '62' because it was < 2 characters long 740s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '63' because it was < 2 characters long 740s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '65' because it was < 2 characters long 740s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '69' because it was < 2 characters long 740s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '75' because it was < 2 characters long 740s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '76' because it was < 2 characters long 740s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '79' because it was < 2 characters long 740s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '80' because it was < 2 characters long 740s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '82' because it was < 2 characters long 740s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '88' because it was < 2 characters long 740s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '90' because it was < 2 characters long 740s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '100' because it was < 2 characters long 740s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '112' because it was < 2 characters long 740s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '113' because it was < 2 characters long 740s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '114' because it was < 2 characters long 740s 115 reads; of these: 740s 115 (100.00%) were unpaired; of these: 740s 100 (86.96%) aligned 0 times 740s 2 (1.74%) aligned exactly 1 time 740s 13 (11.30%) aligned >1 times 740s 13.04% overall alignment rate 740s Read 50 alignments... 740s Read 100 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s AAT 740s AAT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TG 740s TG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s ATG 740s ATG 740s Processing line... 740s Processing line... 740s Processing line... 740s CGTCAACAC 740s CGTCAACAC 740s Processing line... 740s ACATGGATTCAATCATAACACATTT 740s ACATGGATTCAATCATAACACATTT 740s Processing line... 740s CGTCAACAC 740s CGTCAACAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CGTCAACAC 740s CGTCAACAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GTCAACAC 740s GTCAACAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s AAC 740s AAC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TA 740s TA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CG 740s CG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s ACA 740s ACA 740s Processing line... 740s Processing line... 740s CAC 740s CAC 740s Processing line... 740s Processing line... 740s GG 740s GG 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s GTCA 740s GTCA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 15 alignments, 0 edits 740s --------------- 740s PASSED 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 13 SNPs, 1/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 21 740s Reference gaps introduced: 1 740s Read gaps introduced: 0 740s Rearrangements introduced: 1 740s Created read sampler 740s Sampling 26 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s *** Run 31 of 100 740s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --ma 14.710470511294 --mp 4.90278625941688,1.96940331645277 --trim3 8 --score-min L,1.95406504072972,1.51277782050246 --rfg 5.6937813614362 --mm --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 740s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s 26 reads; of these: 740s 22 (84.62%) were paired; of these: 740s 22 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 22 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 22 pairs aligned 0 times concordantly or discordantly; of these: 740s 44 mates make up the pairs; of these: 740s 37 (84.09%) aligned 0 times 740s 1 (2.27%) aligned exactly 1 time 740s 6 (13.64%) aligned >1 times 740s 4 (15.38%) were unpaired; of these: 740s 4 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 14.58% overall alignment rate 740s Read 50 alignments... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TGGCGTCAACACC 740s TGGCGTCAACACC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s CACCT 740s CACCT 740s Processing line... 740s Processing line... 740s CT 740s CT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s ATGCT 740s ATGCT 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s TCA 740s TCA 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s ACAT 740s ACAT 740s Processing line... 740s Processing line... 740s Processing line... 740s GTC 740s GTC 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s Processing line... 740s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --ma 14.710470511294 --mp 4.90278625941688,1.96940331645277 --trim3 8 --score-min L,1.95406504072972,1.51277782050246 --rfg 5.6937813614362 --mm --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 740s Processing line... 740s Processing line... 740s Processing line... 740s --- Summary --- 740s Read 1 reference strings 740s Checked 7 alignments, 0 edits 740s --------------- 740s PASSED 740s ALSO checking that bowtie2 and bowtie2-align match up 740s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 740s 26 reads; of these: 740s 22 (84.62%) were paired; of these: 740s 22 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 22 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 22 pairs aligned 0 times concordantly or discordantly; of these: 740s 44 mates make up the pairs; of these: 740s 37 (84.09%) aligned 0 times 740s 1 (2.27%) aligned exactly 1 time 740s 6 (13.64%) aligned >1 times 740s 4 (15.38%) were unpaired; of these: 740s 4 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 14.58% overall alignment rate 740s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 740s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --ma 14.710470511294 --mp 4.90278625941688,1.96940331645277 --trim3 8 --score-min L,1.95406504072972,1.51277782050246 --rfg 5.6937813614362 --mm --qseq -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 740s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 740s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 740s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 740s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 740s 26 reads; of these: 740s 22 (84.62%) were paired; of these: 740s 22 (100.00%) aligned concordantly 0 times 740s 0 (0.00%) aligned concordantly exactly 1 time 740s 0 (0.00%) aligned concordantly >1 times 740s ---- 740s 22 pairs aligned concordantly 0 times; of these: 740s 0 (0.00%) aligned discordantly 1 time 740s ---- 740s 22 pairs aligned 0 times concordantly or discordantly; of these: 740s 44 mates make up the pairs; of these: 740s 37 (84.09%) aligned 0 times 740s 1 (2.27%) aligned exactly 1 time 740s 6 (13.64%) aligned >1 times 740s 4 (15.38%) were unpaired; of these: 740s 4 (100.00%) aligned 0 times 740s 0 (0.00%) aligned exactly 1 time 740s 0 (0.00%) aligned >1 times 740s 14.58% overall alignment rate 740s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 740s Flattened IUPAC characters 740s Mutating sequence Sim.pm.2 740s Introducing 1 SNPs, 1/1 ref/read gaps, and 3 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutating sequence Sim.pm.1 740s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 740s Finished SNPs 740s Finished ref gaps 740s Finished read gaps 740s Mutated reference genome to subject genome 740s SNPs introduced: 4 740s Reference gaps introduced: 1 740s Read gaps introduced: 1 740s Rearrangements introduced: 3 740s Created read sampler 740s Sampling 40 reads 740s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 740s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 740s parsing sequence Sim.pm.1... 740s parsing sequence Sim.pm.2... 740s Parsed 94 reference bases 740s *** Run 32 of 100 740s /usr/bin/bowtie2 -R 2 --cp-min 3 -M 4 --np 3 --trim3 9 --cp-ival 1 --local --mp 9.84565244795776,6.4821199653578 --score-min L,9.04193948189023,5.85322670104181 --rfg 9.79791112515258 --rdg 5.14680052244945 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 740s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 740s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '6' because it was < 2 characters long 740s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '7' because it was < 2 characters long 740s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '8' because it was < 2 characters long 740s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '11' because it was < 2 characters long 740s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '14' because it was < 2 characters long 740s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '20' because it was < 2 characters long 740s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '24' because it was < 2 characters long 740s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '26' because it was < 2 characters long 740s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '29' because it was < 2 characters long 740s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '34' because it was < 2 characters long 740s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 740s Warning: skipping read '38' because it was < 2 characters long 740s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '39' because it was < 2 characters long 740s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 740s Warning: skipping read '40' because it was < 2 characters long 741s 40 reads; of these: 741s 40 (100.00%) were unpaired; of these: 741s 40 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 0 alignments, 0 edits 741s --------------- 741s PASSED 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.1 741s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.2 741s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 4 741s Reference gaps introduced: 0 741s Read gaps introduced: 0 741s Rearrangements introduced: 1 741s Created read sampler 741s Sampling 100 reads 741s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 741s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s Parsed 94 reference bases 741s *** Run 33 of 100 741s /usr/bin/bowtie2 --trim3 7 --ma 12.4043137041697 --cp-ival 1 --cp-min 8 -k 7 --norc --score-min L,8.50226599382824,5.92207200190803 --np 4 -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta 741s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 741s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 741s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '1' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 741s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 741s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '10' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 741s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '11' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 741s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '20' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 741s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '23' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 741s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '24' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 741s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '30' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 741s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '31' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 741s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '32' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 741s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '38' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 741s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '42' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 741s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '45' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 741s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '51' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 741s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '64' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 741s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '68' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 741s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '71' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 741s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '72' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 741s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '76' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 741s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '82' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 741s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '83' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 741s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '86' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 741s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '90' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 741s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '93' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 741s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '94' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 741s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '95' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 741s 100 reads; of these: 741s 100 (100.00%) were unpaired; of these: 741s 95 (95.00%) aligned 0 times 741s 2 (2.00%) aligned exactly 1 time 741s 3 (3.00%) aligned >1 times 741s 5.00% overall alignment rate 741s Read 50 alignments... 741s Read 100 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s ATAA 741s ATAA 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s TGGC 741s TGGC 741s Processing line... 741s TGGC 741s TGGC 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s GGATTCAATCATAACAC 741s GGATTCAATCATAACAC 741s Processing line... 741s GC 741s GC 741s Processing line... 741s GC 741s GC 741s Processing line... 741s GC 741s GC 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s TC 741s TC 741s Processing line... 741s TC 741s TC 741s Processing line... 741s TC 741s TC 741s Processing line... 741s TC 741s TC 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 11 alignments, 0 edits 741s --------------- 741s PASSED 741s ALSO checking that bowtie2 and bowtie2-align match up 741s /usr/bin/bowtie2 --trim3 7 --ma 12.4043137041697 --cp-ival 1 --cp-min 8 -k 7 --norc --score-min L,8.50226599382824,5.92207200190803 --np 4 -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 741s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 741s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 741s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '1' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 741s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 741s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '10' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 741s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '11' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 741s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '20' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 741s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '23' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 741s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '24' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 741s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '30' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 741s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '31' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 741s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '32' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 741s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '38' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 741s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '42' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 741s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '45' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 741s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '51' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 741s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '64' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 741s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '68' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 741s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '71' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 741s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '72' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 741s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '76' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 741s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '82' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 741s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '83' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 741s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '86' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 741s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '90' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 741s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '93' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 741s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '94' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 741s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '95' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 741s 100 reads; of these: 741s 100 (100.00%) were unpaired; of these: 741s 95 (95.00%) aligned 0 times 741s 2 (2.00%) aligned exactly 1 time 741s 3 (3.00%) aligned >1 times 741s 5.00% overall alignment rate 741s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.1 741s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.2 741s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 8 741s Reference gaps introduced: 1 741s Read gaps introduced: 0 741s Rearrangements introduced: 1 741s Created read sampler 741s Sampling 33 reads 741s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 741s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s Parsed 94 reference bases 741s *** Run 34 of 100 741s /usr/bin/bowtie2 -D 43 --cp-ival 2 --local --cp-min 3 -N 1 --norc --rdg 3.39691528339768,12.8501511464188 --score-min L,8.96722115725922,7.46374628060425 -M 8 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 741s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 741s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '27' because it was < 2 characters long 741s 33 reads; of these: 741s 33 (100.00%) were paired; of these: 741s 33 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 33 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 33 pairs aligned 0 times concordantly or discordantly; of these: 741s 66 mates make up the pairs; of these: 741s 66 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s Read 50 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 0 alignments, 0 edits 741s --------------- 741s PASSED 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.1 741s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s *** Run 35 of 100 741s /usr/bin/bowtie2 -M 5 --trim5 5 --norc --np 1 --cp-min 2 --mm --score-min L,4.37434635349523,3.67021145716681 --mp 5.96153008925266,1.18918620891908 -N 0 -L13 --cp-ival 3 --local -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta 741s Finished read gaps 741s Mutating sequence Sim.pm.2 741s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 4 741s Reference gaps introduced: 0 741s Read gaps introduced: 0 741s Rearrangements introduced: 2 741s Created read sampler 741s Sampling 58 reads 741s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 741s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s Parsed 94 reference bases 741s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 741s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '2' because it was < 2 characters long 741s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '5' because it was < 2 characters long 741s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '10' because it was < 2 characters long 741s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '15' because it was < 2 characters long 741s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '28' because it was < 2 characters long 741s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '36' because it was < 2 characters long 741s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '42' because it was < 2 characters long 741s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '46' because it was < 2 characters long 741s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '55' because it was < 2 characters long 741s 58 reads; of these: 741s 58 (100.00%) were unpaired; of these: 741s 58 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s Read 50 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 0 alignments, 0 edits 741s --------------- 741s PASSED 741s ALSO checking that bowtie2 and bowtie2-align match up 741s /usr/bin/bowtie2 -M 5 --trim5 5 --norc --np 1 --cp-min 2 --mm --score-min L,4.37434635349523,3.67021145716681 --mp 5.96153008925266,1.18918620891908 -N 0 -L13 --cp-ival 3 --local -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 741s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 741s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '2' because it was < 2 characters long 741s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '5' because it was < 2 characters long 741s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '10' because it was < 2 characters long 741s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '15' because it was < 2 characters long 741s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '28' because it was < 2 characters long 741s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '36' because it was < 2 characters long 741s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '42' because it was < 2 characters long 741s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '46' because it was < 2 characters long 741s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '55' because it was < 2 characters long 741s 58 reads; of these: 741s 58 (100.00%) were unpaired; of these: 741s 58 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 741s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 741s /usr/bin/bowtie2 -M 5 --trim5 5 --norc --np 1 --cp-min 2 --mm --score-min L,4.37434635349523,3.67021145716681 --mp 5.96153008925266,1.18918620891908 -N 0 -L13 --cp-ival 3 --local -f -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 741s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 741s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '2' because it was < 2 characters long 741s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '5' because it was < 2 characters long 741s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '10' because it was < 2 characters long 741s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '15' because it was < 2 characters long 741s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '28' because it was < 2 characters long 741s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '36' because it was < 2 characters long 741s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '42' because it was < 2 characters long 741s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '46' because it was < 2 characters long 741s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '55' because it was < 2 characters long 741s 58 reads; of these: 741s 58 (100.00%) were unpaired; of these: 741s 58 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.1 741s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.2 741s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 6 741s Reference gaps introduced: 0 741s Read gaps introduced: 2 741s Rearrangements introduced: 1 741s Created read sampler 741s Sampling 41 reads 741s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 741s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 741s parsing sequence Sim.pm.1... 741s *** Run 36 of 100 741s /usr/bin/bowtie2 --norc --np 10 --cp-min 5 -R 4 --score-min L,9.51242376377621,7.08761997821168 --rfg 13.7832775789213,15.2806709748027 --rdg 26.7492253387739 --gbar 7 --mm --mp 9.99682764230778,3.49086793312979 --cp-ival 1 --local --trim3 3 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 741s parsing sequence Sim.pm.2... 741s Parsed 94 reference bases 741s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '1' because it was < 2 characters long 741s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '11' because it was < 2 characters long 741s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '22' because it was < 2 characters long 741s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '27' because it was < 2 characters long 741s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '29' because it was < 2 characters long 741s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '30' because it was < 2 characters long 741s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '31' because it was < 2 characters long 741s 41 reads; of these: 741s 41 (100.00%) were unpaired; of these: 741s 41 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 0 alignments, 0 edits 741s --------------- 741s PASSED 741s ALSO checking that bowtie2 and bowtie2-align match up 741s /usr/bin/bowtie2 --norc --np 10 --cp-min 5 -R 4 --score-min L,9.51242376377621,7.08761997821168 --rfg 13.7832775789213,15.2806709748027 --rdg 26.7492253387739 --gbar 7 --mm --mp 9.99682764230778,3.49086793312979 --cp-ival 1 --local --trim3 3 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 741s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '1' because it was < 2 characters long 741s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '11' because it was < 2 characters long 741s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '22' because it was < 2 characters long 741s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '27' because it was < 2 characters long 741s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '29' because it was < 2 characters long 741s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '30' because it was < 2 characters long 741s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '31' because it was < 2 characters long 741s 41 reads; of these: 741s 41 (100.00%) were unpaired; of these: 741s 41 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 741s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 741s /usr/bin/bowtie2 --norc --np 10 --cp-min 5 -R 4 --score-min L,9.51242376377621,7.08761997821168 --rfg 13.7832775789213,15.2806709748027 --rdg 26.7492253387739 --gbar 7 --mm --mp 9.99682764230778,3.49086793312979 --cp-ival 1 --local --trim3 3 -r -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 741s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '1' because it was < 2 characters long 741s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '11' because it was < 2 characters long 741s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '22' because it was < 2 characters long 741s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '27' because it was < 2 characters long 741s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '29' because it was < 2 characters long 741s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 741s Warning: skipping read '30' because it was < 2 characters long 741s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 741s Warning: skipping read '31' because it was < 2 characters long 741s 41 reads; of these: 741s 41 (100.00%) were unpaired; of these: 741s 41 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.1 741s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.2 741s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 3 741s Reference gaps introduced: 1 741s Read gaps introduced: 0 741s Rearrangements introduced: 0 741s Created read sampler 741s Sampling 81 reads 741s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 741s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s *** Run 37 of 100 741s /usr/bin/bowtie2 -i L --norc -R 4 --cp-min 3 --gbar 5 --score-min L,9.27656254801332,1.76322173786994 --rfg 35.7354671408025,16.292587762638 --rdg 18.0036896021634 --trim3 9 --local --cp-ival 1 -N 1 -L22 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 741s Parsed 94 reference bases 741s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '2' because it was < 2 characters long 741s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '14' because it was < 2 characters long 741s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '16' because it was < 2 characters long 741s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 741s Warning: skipping read '18' because it was < 2 characters long 741s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '21' because it was < 2 characters long 741s Warning: skipping read '30' because length (1) <= # seed mismatches (1) 741s Warning: skipping read '30' because it was < 2 characters long 741s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '35' because it was < 2 characters long 741s Warning: skipping mate #2 of read '35' because it was < 2 characters long 741s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '41' because it was < 2 characters long 741s Warning: skipping mate #2 of read '41' because it was < 2 characters long 741s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '48' because it was < 2 characters long 741s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '49' because it was < 2 characters long 741s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '50' because it was < 2 characters long 741s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '51' because it was < 2 characters long 741s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '52' because it was < 2 characters long 741s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '60' because it was < 2 characters long 741s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '70' because it was < 2 characters long 741s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '72' because it was < 2 characters long 741s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '77' because it was < 2 characters long 741s Read 50 alignments... 741s 81 reads; of these: 741s 65 (80.25%) were paired; of these: 741s 65 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 65 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 65 pairs aligned 0 times concordantly or discordantly; of these: 741s 130 mates make up the pairs; of these: 741s 130 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 16 (19.75%) were unpaired; of these: 741s 16 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s Read 100 alignments... 741s Read 150 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 0 alignments, 0 edits 741s --------------- 741s PASSED 741s ALSO checking that bowtie2 and bowtie2-align match up 741s /usr/bin/bowtie2 -i L --norc -R 4 --cp-min 3 --gbar 5 --score-min L,9.27656254801332,1.76322173786994 --rfg 35.7354671408025,16.292587762638 --rdg 18.0036896021634 --trim3 9 --local --cp-ival 1 -N 1 -L22 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 741s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '2' because it was < 2 characters long 741s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '14' because it was < 2 characters long 741s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '16' because it was < 2 characters long 741s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 741s Warning: skipping read '18' because it was < 2 characters long 741s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '21' because it was < 2 characters long 741s Warning: skipping read '30' because length (1) <= # seed mismatches (1) 741s Warning: skipping read '30' because it was < 2 characters long 741s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '35' because it was < 2 characters long 741s Warning: skipping mate #2 of read '35' because it was < 2 characters long 741s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '41' because it was < 2 characters long 741s Warning: skipping mate #2 of read '41' because it was < 2 characters long 741s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '48' because it was < 2 characters long 741s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '49' because it was < 2 characters long 741s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '50' because it was < 2 characters long 741s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '51' because it was < 2 characters long 741s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '52' because it was < 2 characters long 741s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '60' because it was < 2 characters long 741s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '70' because it was < 2 characters long 741s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '72' because it was < 2 characters long 741s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '77' because it was < 2 characters long 741s 81 reads; of these: 741s 65 (80.25%) were paired; of these: 741s 65 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 65 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 65 pairs aligned 0 times concordantly or discordantly; of these: 741s 130 mates make up the pairs; of these: 741s 130 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 16 (19.75%) were unpaired; of these: 741s 16 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 741s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 741s /usr/bin/bowtie2 -i L --norc -R 4 --cp-min 3 --gbar 5 --score-min L,9.27656254801332,1.76322173786994 --rfg 35.7354671408025,16.292587762638 --rdg 18.0036896021634 --trim3 9 --local --cp-ival 1 -N 1 -L22 -q -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 741s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '2' because it was < 2 characters long 741s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 741s Warning: skipping read '8' because it was < 2 characters long 741s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '14' because it was < 2 characters long 741s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '16' because it was < 2 characters long 741s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 741s Warning: skipping read '18' because it was < 2 characters long 741s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '21' because it was < 2 characters long 741s Warning: skipping read '30' because length (1) <= # seed mismatches (1) 741s Warning: skipping read '30' because it was < 2 characters long 741s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '35' because it was < 2 characters long 741s Warning: skipping mate #2 of read '35' because it was < 2 characters long 741s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '41' because it was < 2 characters long 741s Warning: skipping mate #2 of read '41' because it was < 2 characters long 741s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '48' because it was < 2 characters long 741s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '49' because it was < 2 characters long 741s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '50' because it was < 2 characters long 741s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '51' because it was < 2 characters long 741s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '52' because it was < 2 characters long 741s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '60' because it was < 2 characters long 741s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '70' because it was < 2 characters long 741s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #2 of read '72' because it was < 2 characters long 741s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '77' because it was < 2 characters long 741s 81 reads; of these: 741s 65 (80.25%) were paired; of these: 741s 65 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 65 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 65 pairs aligned 0 times concordantly or discordantly; of these: 741s 130 mates make up the pairs; of these: 741s 130 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 16 (19.75%) were unpaired; of these: 741s 16 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 0.00% overall alignment rate 741s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.2 741s Introducing 3 SNPs, 2/0 ref/read gaps, and 1 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.1 741s Introducing 2 SNPs, 0/2 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 5 741s Reference gaps introduced: 2 741s Read gaps introduced: 2 741s Rearrangements introduced: 1 741s Created read sampler 741s Sampling 74 reads 741s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 741s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s Parsed 94 reference bases 741s *** Run 38 of 100 741s /usr/bin/bowtie2 -N 1 -L25 --cp-ival 4 --trim3 1 --rdg 1.81455056426898 --score-min L,8.59403514279658,4.65072217877553 --mm -a --ma 15.6789796253262 --cp-min 2 -R 4 --norc -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 741s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 741s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '6' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 741s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '14' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 741s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '39' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 741s Read 50 alignments... 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 741s Read 100 alignments... 741s 74 reads; of these: 741s 72 (97.30%) were paired; of these: 741s 72 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 72 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 72 pairs aligned 0 times concordantly or discordantly; of these: 741s 144 mates make up the pairs; of these: 741s 138 (95.83%) aligned 0 times 741s 1 (0.69%) aligned exactly 1 time 741s 5 (3.47%) aligned >1 times 741s 2 (2.70%) were unpaired; of these: 741s 2 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 4.11% overall alignment rate 741s Read 150 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s /usr/bin/bowtie2 -N 1 -L25 --cp-ival 4 --trim3 1 --rdg 1.81455056426898 --score-min L,8.59403514279658,4.65072217877553 --mm -a --ma 15.6789796253262 --cp-min 2 -R 4 --norc -q -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s CAAC 741s CAAC 741s Processing line... 741s CAAC 741s CAAC 741s Processing line... 741s TGCT 741s TGCT 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s CAT 741s CAT 741s Processing line... 741s CAT 741s CAT 741s Processing line... 741s CAT 741s CAT 741s Processing line... 741s CAT 741s CAT 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s CC 741s CC 741s Processing line... 741s CC 741s CC 741s Processing line... 741s CC 741s CC 741s Processing line... 741s CC 741s CC 741s Processing line... 741s CC 741s CC 741s Processing line... 741s CC 741s CC 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s TG 741s TG 741s Processing line... 741s TG 741s TG 741s Processing line... 741s TG 741s TG 741s Processing line... 741s TG 741s TG 741s Processing line... 741s TG 741s TG 741s Processing line... 741s TG 741s TG 741s Processing line... 741s TG 741s TG 741s Processing line... 741s Processing line... 741s TCAA 741s TCAA 741s Processing line... 741s TCAA 741s TCAA 741s Processing line... 741s TCAA 741s TCAA 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s --- Summary --- 741s Read 1 reference strings 741s Checked 23 alignments, 0 edits 741s --------------- 741s PASSED 741s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 741s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 741s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '6' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 741s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '14' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 741s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (1) 741s Warning: skipping mate #1 of read '39' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 741s 74 reads; of these: 741s 72 (97.30%) were paired; of these: 741s 72 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 72 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 72 pairs aligned 0 times concordantly or discordantly; of these: 741s 144 mates make up the pairs; of these: 741s 138 (95.83%) aligned 0 times 741s 1 (0.69%) aligned exactly 1 time 741s 5 (3.47%) aligned >1 times 741s 2 (2.70%) were unpaired; of these: 741s 2 (100.00%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 0 (0.00%) aligned >1 times 741s 4.11% overall alignment rate 741s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 741s Flattened IUPAC characters 741s Mutating sequence Sim.pm.1 741s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutating sequence Sim.pm.2 741s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 741s Finished SNPs 741s Finished ref gaps 741s Finished read gaps 741s Mutated reference genome to subject genome 741s SNPs introduced: 9 741s Reference gaps introduced: 0 741s Read gaps introduced: 1 741s Rearrangements introduced: 0 741s Created read sampler 741s Sampling 78 reads 741s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 741s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 741s parsing sequence Sim.pm.1... 741s parsing sequence Sim.pm.2... 741s Parsed 94 reference bases 741s *** Run 39 of 100 741s /usr/bin/bowtie2 --score-min L,2.68163896209528,6.59738708090871 --rfg 41.8147964325071,18.5604030860748 --cp-min 7 --cp-ival 1 -D 9 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 741s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 741s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 741s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 741s Read 50 alignments... 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 741s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 741s Read 100 alignments... 741s 78 reads; of these: 741s 78 (100.00%) were paired; of these: 741s 78 (100.00%) aligned concordantly 0 times 741s 0 (0.00%) aligned concordantly exactly 1 time 741s 0 (0.00%) aligned concordantly >1 times 741s ---- 741s 78 pairs aligned concordantly 0 times; of these: 741s 0 (0.00%) aligned discordantly 1 time 741s ---- 741s 78 pairs aligned 0 times concordantly or discordantly; of these: 741s 156 mates make up the pairs; of these: 741s 148 (94.87%) aligned 0 times 741s 0 (0.00%) aligned exactly 1 time 741s 8 (5.13%) aligned >1 times 741s 5.13% overall alignment rate 741s Read 150 alignments... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s TTG 741s TTG 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 741s Processing line... 742s Processing line... 742s GTCAA 742s GTCAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s /usr/bin/bowtie2 --score-min L,2.68163896209528,6.59738708090871 --rfg 41.8147964325071,18.5604030860748 --cp-min 7 --cp-ival 1 -D 9 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CCGAAA 742s CCGAAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AA 742s AA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CCG 742s CCG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CCT 742s CCT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CG 742s CG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATC 742s ATC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 8 alignments, 0 edits 742s --------------- 742s PASSED 742s ALSO checking that bowtie2 and bowtie2-align match up 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s 78 reads; of these: 742s 78 (100.00%) were paired; of these: 742s 78 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 78 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 78 pairs aligned 0 times concordantly or discordantly; of these: 742s 156 mates make up the pairs; of these: 742s 148 (94.87%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 8 (5.13%) aligned >1 times 742s 5.13% overall alignment rate 742s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 742s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 742s /usr/bin/bowtie2 --score-min L,2.68163896209528,6.59738708090871 --rfg 41.8147964325071,18.5604030860748 --cp-min 7 --cp-ival 1 -D 9 --qseq -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 742s *** Run 40 of 100 742s /usr/bin/bowtie2 --cp-ival 1 --cp-min 2 -M 2 --trim5 4 --norc --rdg 28.5362702033403,2.99993649776774 --score-min L,2.07019746627975,5.89023202968283 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s 78 reads; of these: 742s 78 (100.00%) were paired; of these: 742s 78 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 78 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 78 pairs aligned 0 times concordantly or discordantly; of these: 742s 156 mates make up the pairs; of these: 742s 148 (94.87%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 8 (5.13%) aligned >1 times 742s 5.13% overall alignment rate 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.1 742s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.2 742s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 6 742s Reference gaps introduced: 0 742s Read gaps introduced: 1 742s Rearrangements introduced: 0 742s Created read sampler 742s Sampling 42 reads 742s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 742s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 94 reference bases 742s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 742s *** Run 41 of 100 742s /usr/bin/bowtie2 --nofw --cp-ival 1 --cp-min 3 --rfg 14.3245201602505 --rdg 1.98332645212428,9.51911967765781 --score-min L,8.75942775120556,3.73949694626836 --gbar 1 --np 4 --trim5 0 -a --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 742s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 742s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '3' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 742s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '6' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 742s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '17' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 742s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '19' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 742s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '29' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 742s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '32' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 742s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '36' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 742s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '39' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 742s 42 reads; of these: 742s 42 (100.00%) were unpaired; of these: 742s 39 (92.86%) aligned 0 times 742s 1 (2.38%) aligned exactly 1 time 742s 2 (4.76%) aligned >1 times 742s 7.14% overall alignment rate 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CGTCAAC 742s CGTCAAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATG 742s ATG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TGGATTCAATCATAAC 742s TGGATTCAATCATAAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 3 alignments, 0 edits 742s --------------- 742s PASSED 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.2 742s Introducing 4 SNPs, 0/1 ref/read gaps, and 2 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.1 742s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 5 742s Reference gaps introduced: 0 742s Read gaps introduced: 1 742s Rearrangements introduced: 2 742s Created read sampler 742s Sampling 117 reads 742s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 742s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 94 reference bases 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: skipping mate #2 of read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 742s Read 50 alignments... 742s Read 100 alignments... 742s Read 150 alignments... 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 742s Read 200 alignments... 742s 117 reads; of these: 742s 117 (100.00%) were paired; of these: 742s 117 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 117 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 117 pairs aligned 0 times concordantly or discordantly; of these: 742s 234 mates make up the pairs; of these: 742s 219 (93.59%) aligned 0 times 742s 2 (0.85%) aligned exactly 1 time 742s 13 (5.56%) aligned >1 times 742s 6.41% overall alignment rate 742s Read 250 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GGCGTCAAC 742s GGCGTCAAC 742s Processing line... 742s GGCGTCAAC 742s GGCGTCAAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATT 742s ATT 742s Processing line... 742s ATT 742s ATT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CCCGAAA 742s CCCGAAA 742s Processing line... 742s CCCGAAA 742s CCCGAAA 742s Processing line... 742s Processing line... 742s GAA 742s GAA 742s Processing line... 742s GAA 742s GAA 742s Processing line... 742s GAA 742s GAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CG 742s CG 742s Processing line... 742s CG 742s CG 742s Processing line... 742s CG 742s CG 742s Processing line... 742s CG 742s CG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GA 742s GA 742s Processing line... 742s GA 742s GA 742s Processing line... 742s GA 742s GA 742s Processing line... 742s GA 742s GA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GGCG 742s GGCG 742s Processing line... 742s GGCG 742s GGCG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATGC 742s ATGC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AACACA 742s AACACA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s Processing line... 742s TTGGCGTCAA 742s TTGGCGTCAA 742s Processing line... 742s TTGGCGTCAA 742s TTGGCGTCAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GCGTCAAC 742s GCGTCAAC 742s Processing line... 742s GCGTCAAC 742s GCGTCAAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CCC 742s CCC 742s Processing line... 742s CCC 742s CCC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Process/usr/bin/bowtie2 --nofw --cp-ival 1 --cp-min 3 --rfg 14.3245201602505 --rdg 1.98332645212428,9.51911967765781 --score-min L,8.75942775120556,3.73949694626836 --gbar 1 --np 4 --trim5 0 -a --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 742s ing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 35 alignments, 0 edits 742s --------------- 742s PASSED 742s ALSO checking that bowtie2 and bowtie2-align match up 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: skipping mate #2 of read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 742s 117 reads; of these: 742s 117 (100.00%) were paired; of these: 742s 117 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 117 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 117 pairs aligned 0 times concordantly or discordantly; of these: 742s 234 mates make up the pairs; of these: 742s 219 (93.59%) aligned 0 times 742s 2 (0.85%) aligned exactly 1 time 742s 13 (5.56%) aligned >1 times 742s 6.41% overall alignment rate 742s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.1 742s Introducing 2 SNPs, 1/1 ref/read gaps, and 1 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.2 742s Introducing 9 SNPs, 1/0 ref/read gaps, and 1 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 11 742s Reference gaps introduced: 2 742s Read gaps introduced: 1 742s Rearrangements introduced: 2 742s Created read sampler 742s Sampling 53 reads 742s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 742s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 94 reference bases 742s *** Run 42 of 100 742s /usr/bin/bowtie2 --cp-ival 2 --trim3 6 --rdg 9.09748666700272 --score-min L,7.3313242374745,2.67811138352354 --mm --cp-min 3 --ma 28.0874706546008 --np 6 -k 3 --trim5 0 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 742s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 742s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 742s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '0' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 742s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '7' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 742s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '13' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 742s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '14' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 742s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '30' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 742s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '31' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 742s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '34' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 742s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '35' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 742s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '39' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 742s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '45' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 742s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '50' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 742s 53 reads; of these: 742s 53 (100.00%) were unpaired; of these: 742s 47 (88.68%) aligned 0 times 742s 3 (5.66%) aligned exactly 1 time 742s 3 (5.66%) aligned >1 times 742s 11.32% overall alignment rate 742s Read 50 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATTCAATCAT 742s ATTCAATCAT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TTCAAT 742s TTCAAT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ACA 742s ACA 742s Processing line... 742s ACA 742s ACA 742s Processing line... 742s ACA 742s ACA 742s Processing line... 742s Processing line... 742s CACCTG 742s CACCTG 742s Processing line... 742s CACCTG 742s CACCTG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATA 742s ATA 742s --- Summary --- 742s Read 1 reference strings 742s Checked 11 alignments, 0 edits 742s --------------- 742s PASSED 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.2 742s Introducing 0 SNPs, 1/1 ref/read gaps, and 1 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.1 742s Introducing 7 SNPs, 0/2 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 7 742s Reference gaps introduced: 1 742s Read gaps introduced: 3 742s Rearrangements introduced: 1 742s Created read sampler 742s Sampling 81 reads 742s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 742s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 94 reference bases 742s *** Run 43 of 100 742s /usr/bin/bowtie2 --trim5 2 --ma 16.0161989435446 --cp-min 5 --score-min L,9.62458530864201,6.32686619543639 --mm -a --mp 9.66384695769613,8.55038227736135 --cp-ival 1 -D 4 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 742s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 742s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 742s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '5' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 742s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '10' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 742s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '19' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 742s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '23' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 742s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '29' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 742s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '41' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 742s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '43' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 742s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '53' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 742s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '54' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 742s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '56' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 742s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '79' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 742s 81 reads; of these: 742s 81 (100.00%) were unpaired; of these: 742s 70 (86.42%) aligned 0 times 742s 1 (1.23%) aligned exactly 1 time 742s 10 (12.35%) aligned >1 times 742s 13.58% overall alignment rate 742s Read 50 alignments... 742s Read 100 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TTGGCGTCAACA 742s TTGGCGTCAACA 742s Processing line... 742s TTGGCGTCAACA 742s TTGGCGTCAACA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TAACA 742s TAACA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CAACACC 742s CAACACC 742s Processing line... 742s CAACACC 742s CAACACC 742s Processing line... 742s CAACAC 742s CAACAC 742s Processing line... 742s CAACAC 742s CAACAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TTT 742s TTT 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GGCGTCAACACC 742s GGCGTCAACACC 742s Processing line... 742s GGCGTCAACACC 742s GGCGTCAACACC 742s Processing line... 742s CCT 742s CCT 742s Processing line... 742s CCT 742s CCT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CAA 742s CAA 742s Processing line... 742s CAA 742s CAA 742s Processing line... 742s CAA 742s CAA 742s Processing line... 742s TTG 742s TTG 742s Processing line... 742s TTG 742s TTG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s Processing line... 742s Processing line... 742s CCC 742s CCC 742s Processing line... 742s CCC 742s CCC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 53 alignments, 0 edits 742s --------------- 742s PASSED 742s ALSO checking that bowtie2 and bowtie2-align match up 742s /usr/bin/bowtie2 --trim5 2 --ma 16.0161989435446 --cp-min 5 --score-min L,9.62458530864201,6.32686619543639 --mm -a --mp 9.66384695769613,8.55038227736135 --cp-ival 1 -D 4 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 742s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 742s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 742s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '5' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 742s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '10' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 742s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '19' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 742s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '23' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 742s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '29' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 742s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '41' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 742s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '43' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 742s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '53' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 742s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 742s Warning: skipping read '54' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 742s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '56' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 742s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 742s Warning: skipping read '79' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 742s 81 reads; of these: 742s 81 (100.00%) were unpaired; of these: 742s 70 (86.42%) aligned 0 times 742s 1 (1.23%) aligned exactly 1 time 742s 10 (12.35%) aligned >1 times 742s 13.58% overall alignment rate 742s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.1 742s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.2 742s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 11 742s Reference gaps introduced: 0 742s Read gaps introduced: 0 742s Rearrangements introduced: 0 742s Created read sampler 742s Sampling 137 reads 742s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 742s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 94 reference bases 742s *** Run 44 of 100 742s /usr/bin/bowtie2 --nofw --cp-ival 1 --n-ceil 0.105362544979815,1.49242472688486 --cp-min 5 --rfg 16.0340059305963,13.2811370677765 --score-min L,3.62950902176475,5.38628863489001 --trim5 0 --mm -k 4 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 742s /usr/bin/bowtie2 --nofw --cp-ival 1 --n-ceil 0.105362544979815,1.49242472688486 --cp-min 5 --rfg 16.0340059305963,13.2811370677765 --score-min L,3.62950902176475,5.38628863489001 --trim5 0 --mm -k 4 --qseq -p 3 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 742s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 742s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 742s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 742s Read 50 alignments... 742s 137 reads; of these: 742s 137 (100.00%) were unpaired; of these: 742s 119 (86.86%) aligned 0 times 742s 2 (1.46%) aligned exactly 1 time 742s 16 (11.68%) aligned >1 times 742s 13.14% overall alignment rate 742s Read 100 alignments... 742s Read 150 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GT 742s GT 742s Processing line... 742s GT 742s GT 742s Processing line... 742s Processing line... 742s CCCGAA 742s CCCGAA 742s Processing line... 742s CCCGAA 742s CCCGAA 742s Processing line... 742s TCAACACCT 742s TCAACACCT 742s Processing line... 742s TCAACACCT 742s TCAACACCT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TAACACA 742s TAACACA 742s Processing line... 742s Processing line... 742s Processing line... 742s ACC 742s ACC 742s Processing line... 742s ACC 742s ACC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATG 742s ATG 742s Processing line... 742s ATG 742s ATG 742s Processing line... 742s ATG 742s ATG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CC 742s CC 742s Processing line... 742s CC 742s CC 742s Processing line... 742s CC 742s CC 742s Processing line... 742s CC 742s CC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ACCT 742s ACCT 742s Processing line... 742s ACCT 742s ACCT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TGGATTCAATC 742s TGGATTCAATC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CGA 742s CGA 742s Processing line... 742s CGA 742s CGA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GAAA 742s GAAA 742s Processing line... 742s GAAA 742s GAAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GTC 742s GTC 742s Processing line... 742s GTC 742s GTC 742s Processing line... 742s Processing line... 742s Processing line... 742s CACC 742s CACC 742s Processing line... 742s CACC 742s CACC 742s Processing line... 742s Processing line... 742s Processing line... 742s GTCAACAC 742s GTCAACAC 742s Processing line... 742s GTCAACAC 742s GTCAACAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ACAC 742s ACAC 742s Processing line... 742s ACAC 742s ACAC 742s Processing line... 742s ACAC 742s ACAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 44 alignments, 0 edits 742s --------------- 742s PASSED 742s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 742s 137 reads; of these: 742s 137 (100.00%) were unpaired; of these: 742s 119 (86.86%) aligned 0 times 742s 2 (1.46%) aligned exactly 1 time 742s 16 (11.68%) aligned >1 times 742s 13.14% overall alignment rate 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.1 742s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.2 742s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 2 742s Reference gaps introduced: 1 742s Read gaps introduced: 1 742s Rearrangements introduced: 0 742s Created read sampler 742s Sampling 178 reads 742s *** Run 45 of 100 742s /usr/bin/bowtie2 --mp 9.52086828428964,2.62859901014292 --cp-min 4 --cp-ival 1 -i S,0.560826100255465,6.4721945976543 --trim5 1 -a --score-min L,5.6116894236736,6.22879317190844 --rfg 24.9487360034336 --np 5 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 742s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 742s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 94 reference bases 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 742s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '11' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 742s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '30' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 742s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '37' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 742s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '45' because it was < 2 characters long 742s Warning: skipping mate #2 of read '45' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 742s Read 50 alignments... 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 742s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '70' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 742s Read 100 alignments... 742s Read 150 alignments... 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 742s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '109' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 742s Warning: skipping mate #2 of read '112' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '112' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 742s Read 200 alignments... 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 742s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '152' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 742s Warning: skipping mate #1 of read '153' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '153' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 742s Warning: skipping mate #1 of read '154' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '154' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 742s Warning: skipping mate #2 of read '174' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '174' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 742s Warning: skipping mate #1 of read '176' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '176' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 742s Read 250 alignments... 742s 178 reads; of these: 742s 175 (98.31%) were paired; of these: 742s 175 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 175 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 175 pairs aligned 0 times concordantly or discordantly; of these: 742s 350 mates make up the pairs; of these: 742s 324 (92.57%) aligned 0 times 742s 6 (1.71%) aligned exactly 1 time 742s 20 (5.71%) aligned >1 times 742s 3 (1.69%) were unpaired; of these: 742s 1 (33.33%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 2 (66.67%) aligned >1 times 742s 7.93% overall alignment rate 742s Read 300 alignments... 742s Read 350 alignments... 742s Read 400 alignments... 742s Read 450 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AC 742s AC 742s Processing line... 742s GT 742s GT 742s Processing line... 742s AC 742s AC 742s Processing line... 742s GT 742s GT 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CGA 742s CGA 742s Processing line... 742s CGA 742s CGA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AATCATAACACATT 742s AATCATAACACATT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TAACACAT 742s TAACACAT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATAACACA 742s ATAACACA 742s Processing line... 742s Processing line... 742s TAACA 742s TAACA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CACCT 742s CACCT 742s Processing line... 742s CACCT 742s CACCT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CACCT 742s CACCT 742s Processing line... 742s CACCT 742s CACCT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CACAT 742s CACAT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CGTCAACA 742s CGTCAACA 742s Processing line... 742s CGTCAACA 742s CGTCAACA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ACC 742s ACC 742s Processing line... 742s ACC 742s ACC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ACA 742s ACA 742s Processing line... 742s ACA 742s ACA 742s Processing line... 742s ACA 742s ACA 742s Processing line... 742s ACA 742s ACA 742s Processing line... 742s ACA 742s ACA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TTGGCGTCAACA 742s TTGGCGTCAACA 742s Processing line... 742s TTGGCGTCAACA 742s TTGGCGTCAACA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CCCGAAA 742s CCCGAAA 742s Processing line... 742s CCCGAAA 742s CCCGAAA 742s Processing line... 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s GT 742s GT 742s Processing line... 742s AC 742s AC 742s Processing line... 742s AC 742s AC 742s Processing line... 742s GT 742s GT 742s Processing line... 742s AC 742s AC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s ATGAACATGGATTCAATCATAACACAT 742s ATGAACATGGATTCAATCATAACACAT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TTGGC 742s TTGGC 742s Processing line... 742s TTGGC 742s TTGGC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s GC 742s GC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s AT 742s AT 742s Processing line... 742s Processing line... 742s GTCAACAC 742s GTCAACAC 742s Processing line... 742s GTCAACAC 742s GTCAACAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TGGCGTCA 742s TGGCGTCA 742s Processing line... 742s TGGCGTCA 742s TGGCGTCA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GTCAA 742s GTCAA 742s Processing line... 742s GTCAA 742s GTCAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s TG 742s TG 742s Processing line... 742s CA 742s CA 742s Processing line... 742s TG 742s TG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TTT 742s TTT 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CCC 742s CCC 742s Processing line... 742s CCC 742s CCC 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 128 alignments, 0 edits 742s --------------- 742s PASSED 742s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 742s /usr/bin/bowtie2 --mp 9.52086828428964,2.62859901014292 --cp-min 4 --cp-ival 1 -i S,0.560826100255465,6.4721945976543 --trim5 1 -a --score-min L,5.6116894236736,6.22879317190844 --rfg 24.9487360034336 --np 5 -f -p 3 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 742s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '11' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 742s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '30' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 742s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '37' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 742s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '45' because it was < 2 characters long 742s Warning: skipping mate #2 of read '45' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 742s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '70' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 742s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '109' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 742s Warning: skipping mate #2 of read '112' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '112' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 742s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '152' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 742s Warning: skipping mate #1 of read '153' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '153' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 742s Warning: skipping mate #1 of read '154' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '154' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 742s Warning: skipping mate #2 of read '174' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #2 of read '174' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 742s Warning: skipping mate #1 of read '176' because length (1) <= # seed mismatches (0) 742s Warning: skipping mate #1 of read '176' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 742s 178 reads; of these: 742s 175 (98.31%) were paired; of these: 742s 175 (100.00%) aligned concordantly 0 times 742s 0 (0.00%) aligned concordantly exactly 1 time 742s 0 (0.00%) aligned concordantly >1 times 742s ---- 742s 175 pairs aligned concordantly 0 times; of these: 742s 0 (0.00%) aligned discordantly 1 time 742s ---- 742s 175 pairs aligned 0 times concordantly or discordantly; of these: 742s 350 mates make up the pairs; of these: 742s 324 (92.57%) aligned 0 times 742s 6 (1.71%) aligned exactly 1 time 742s 20 (5.71%) aligned >1 times 742s 3 (1.69%) were unpaired; of these: 742s 1 (33.33%) aligned 0 times 742s 0 (0.00%) aligned exactly 1 time 742s 2 (66.67%) aligned >1 times 742s 7.93% overall alignment rate 742s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 742s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 742s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 742s Flattened IUPAC characters 742s Mutating sequence Sim.pm.1 742s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutating sequence Sim.pm.2 742s Introducing 4 SNPs, 2/0 ref/read gaps, and 1 rearrangements 742s Finished SNPs 742s Finished ref gaps 742s Finished read gaps 742s Mutated reference genome to subject genome 742s SNPs introduced: 4 742s Reference gaps introduced: 2 742s Read gaps introduced: 1 742s Rearrangements introduced: 1 742s Created read sampler 742s Sampling 189 reads 742s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 742s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 742s parsing sequence Sim.pm.1... 742s parsing sequence Sim.pm.2... 742s Parsed 94 reference bases 742s *** Run 46 of 100 742s /usr/bin/bowtie2 --trim3 2 --cp-ival 1 --n-ceil 0.76699436418457,0.892428114012065 --mp 5.57486343843089,3.22278773222908 -a --score-min L,2.1438986930211,7.16151928190568 --rfg 29.2096615367668,7.40876957902006 --rdg 44.8303787915885,6.59497045286581 --cp-min 2 --ma 28.2316503178749 --trim5 3 --np 6 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 742s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_149_149_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_151_151_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_156_156_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_157_157_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_157_157_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_158_158_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_159_159_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_159_159_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_159_159_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 742s Read 50 alignments... 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_161_161_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_162_162_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_163_163_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_165_165_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_166_166_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_167_167_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_168_168_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_169_169_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_170_170_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_171_171_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_172_172_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_173_173_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_174_174_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_175_175_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_177_177_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_178_178_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_179_179_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_180_180_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_180_180_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_180_180_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_181_181_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_182_182_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_183_183_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_184_184_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_185_185_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_186_186_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_187_187_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_188_188_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_189_189_1/1; setting to 0 instead 742s Read 100 alignments... 742s Read 150 alignments... 742s 189 reads; of these: 742s 189 (100.00%) were unpaired; of these: 742s 168 (88.89%) aligned 0 times 742s 8 (4.23%) aligned exactly 1 time 742s 13 (6.88%) aligned >1 times 742s 11.11% overall alignment rate 742s Read 200 alignments... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TGGC 742s TGGC 742s Processing line... 742s TGGC 742s TGGC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CATGGA 742s CATGGA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CAT 742s CAT 742s Processing line... 742s ATG 742s ATG 742s Processing line... 742s CAT 742s CAT 742s Processing line... 742s ATG 742s ATG 742s Processing line... 742s CAT 742s CAT 742s Processing line... 742s ATG 742s ATG 742s Processing line... 742s CAT 742s CAT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AACACCT 742s AACACCT 742s Processing line... 742s AACACCT 742s AACACCT 742s Processing line... 742s CAC 742s CAC 742s Processing line... 742s CAC 742s CAC 742s Processing line... 742s CAC 742s CAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CATT 742s CATT 742s Processing line... 742s TGAACA 742s TGAACA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s AA 742s AA 742s Processing line... 742s AA 742s AA 742s Processing line... 742s TT 742s TT 742s Processing line... 742s TT 742s TT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AACAC 742s AACAC 742s Processing line... 742s AACAC 742s AACAC 742s Processing line... 742s AACAC 742s AACAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TGG 742s TGG 742s Processing line... 742s TGG 742s TGG 742s Processing line... 742s TGG 742s TGG 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s TA 742s TA 742s Processing line... 742s TA 742s TA 742s Processing line... 742s TA 742s TA 742s Processing line... 742s TA 742s TA 742s Processing line... 742s Processing line... 742s Processing line... 742s TA 742s TA 742s Processing line... 742s TA 742s TA 742s Processing line... 742s TA 742s TA 742s Processing line... 742s TA 742s TA 742s Processing line... 742s AACATGGATTCAATCATAAC 742s AACATGGATTCAATCATAAC 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s TTT 742s TTT 742s Processing line... 742s Processing line... 742s Processing line... 742s CATGA 742s CATGA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GCTA 742s GCTA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s GCTA 742s GCTA 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s CCG 742s CCG 742s Processing line... 742s CCG 742s CCG 742s Processing line... 742s Processing line... 742s Processing line... 742s ACATGGATTCAAT 742s ACATGGATTCAAT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s AACACCT 742s AACACCT 742s Processing line... 742s AACACCT 742s AACACCT 742s /usr/bin/bowtie2 --trim3 2 --cp-ival 1 --n-ceil 0.76699436418457,0.892428114012065 --mp 5.57486343843089,3.22278773222908 -a --score-min L,2.1438986930211,7.16151928190568 --rfg 29.2096615367668,7.40876957902006 --rdg 44.8303787915885,6.59497045286581 --cp-min 2 --ma 28.2316503178749 --trim5 3 --np 6 --qseq -p 3 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 742s Processing line... 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s AAA 742s AAA 742s Processing line... 742s TTT 742s TTT 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s Processing line... 742s --- Summary --- 742s Read 1 reference strings 742s Checked 60 alignments, 0 edits 742s --------------- 742s PASSED 742s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 742s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_106_106_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 742s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 742s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 742s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_136_136_1/1' because length (1) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_143_143_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_144_144_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_145_145_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_147_147_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_148_148_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_149_149_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_149_149_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_150_150_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_151_151_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_151_151_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_153_153_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_154_154_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_156_156_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_157_157_1/1' because length (1) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_157_157_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_158_158_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_159_159_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_159_159_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_159_159_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_161_161_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_162_162_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_163_163_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_165_165_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_166_166_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_167_167_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_168_168_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_169_169_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_170_170_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_171_171_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_172_172_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_173_173_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_174_174_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_175_175_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_177_177_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_178_178_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_179_179_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_180_180_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_180_180_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_180_180_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_181_181_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_182_182_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_183_183_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_184_184_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_185_185_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_186_186_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_187_187_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_188_188_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_189_189_1/1; setting to 0 instead 743s 189 reads; of these: 743s 189 (100.00%) were unpaired; of these: 743s 168 (88.89%) aligned 0 times 743s 8 (4.23%) aligned exactly 1 time 743s 13 (6.88%) aligned >1 times 743s 11.11% overall alignment rate 743s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 743s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 743s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.1 743s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.2 743s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 15 743s Reference gaps introduced: 0 743s Read gaps introduced: 0 743s Rearrangements introduced: 0 743s Created read sampler 743s Sampling 81 reads 743s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 743s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 94 reference bases 743s *** Run 47 of 100 743s /usr/bin/bowtie2 --trim5 9 -i C,0.796293459220298,8.49043603226871 -k 4 --norc --ma 23.1886341693038 --cp-min 6 --mm --score-min L,2.59497654650966,6.29817475953366 --nofw --mp 7.95846577196829,1.42985910667946 --cp-ival 1 -D 25 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 743s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 743s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '2' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 743s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '3' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 743s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '4' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 743s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '8' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 743s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '19' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 743s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '33' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 743s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '35' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 743s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '46' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 743s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '48' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 743s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '52' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 743s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '53' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 743s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '58' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 743s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '59' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 743s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '60' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 743s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '63' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 743s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '65' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 743s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '73' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 743s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '77' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 743s Read 50 alignments... 743s 81 reads; of these: 743s 69 (85.19%) were paired; of these: 743s 69 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 69 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 69 pairs aligned 0 times concordantly or discordantly; of these: 743s 138 mates make up the pairs; of these: 743s 138 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 12 (14.81%) were unpaired; of these: 743s 12 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s Read 100 alignments... 743s Read 150 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s /usr/bin/bowtie2 --trim5 9 -i C,0.796293459220298,8.49043603226871 -k 4 --norc --ma 23.1886341693038 --cp-min 6 --mm --score-min L,2.59497654650966,6.29817475953366 --nofw --mp 7.95846577196829,1.42985910667946 --cp-ival 1 -D 25 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 0 alignments, 0 edits 743s --------------- 743s PASSED 743s ALSO checking that bowtie2 and bowtie2-align match up 743s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 743s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '2' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 743s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '3' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 743s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '4' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 743s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '8' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 743s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '19' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 743s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '33' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 743s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '35' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 743s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '46' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 743s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '48' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 743s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '52' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 743s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '53' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 743s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '58' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 743s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '59' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 743s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '60' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 743s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '63' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 743s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '65' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 743s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '73' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 743s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '77' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 743s 81 reads; of these: 743s 69 (85.19%) were paired; of these: 743s 69 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 69 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 69 pairs aligned 0 times concordantly or discordantly; of these: 743s 138 mates make up the pairs; of these: 743s 138 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 12 (14.81%) were unpaired; of these: 743s 12 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 743s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 743s /usr/bin/bowtie2 --trim5 9 -i C,0.796293459220298,8.49043603226871 -k 4 --norc --ma 23.1886341693038 --cp-min 6 --mm --score-min L,2.59497654650966,6.29817475953366 --nofw --mp 7.95846577196829,1.42985910667946 --cp-ival 1 -D 25 -q -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 743s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 743s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '2' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 743s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '3' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 743s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '4' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 743s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '8' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 743s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '19' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 743s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '33' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 743s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '35' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 743s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '46' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 743s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '48' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 743s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '52' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 743s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '53' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 743s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '58' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 743s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '59' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 743s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '60' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 743s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '63' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 743s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '65' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 743s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '73' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 743s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '77' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 743s 81 reads; of these: 743s 69 (85.19%) were paired; of these: 743s 69 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 69 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 69 pairs aligned 0 times concordantly or discordantly; of these: 743s 138 mates make up the pairs; of these: 743s 138 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 12 (14.81%) were unpaired; of these: 743s 12 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.1 743s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.2 743s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 7 743s Reference gaps introduced: 2 743s Read gaps introduced: 0 743s Rearrangements introduced: 0 743s Created read sampler 743s Sampling 174 reads 743s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 743s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 94 reference bases 743s *** Run 48 of 100 743s /usr/bin/bowtie2 --trim5 4 --np 6 --cp-min 6 --mm -a --score-min L,3.65754688293277,1.39494813493015 --gbar 7 --trim3 6 --cp-ival 1 --local -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 743s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '2' because it was < 2 characters long 743s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '3' because it was < 2 characters long 743s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '8' because it was < 2 characters long 743s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '14' because it was < 2 characters long 743s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '15' because it was < 2 characters long 743s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '20' because it was < 2 characters long 743s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '26' because it was < 2 characters long 743s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '27' because it was < 2 characters long 743s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '28' because it was < 2 characters long 743s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '31' because it was < 2 characters long 743s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '38' because it was < 2 characters long 743s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '39' because it was < 2 characters long 743s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '44' because it was < 2 characters long 743s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '48' because it was < 2 characters long 743s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '53' because it was < 2 characters long 743s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '58' because it was < 2 characters long 743s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '62' because it was < 2 characters long 743s Read 50 alignments... 743s Read 100 alignments... 743s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '71' because it was < 2 characters long 743s Warning: skipping mate #2 of read '71' because it was < 2 characters long 743s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '74' because it was < 2 characters long 743s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '76' because it was < 2 characters long 743s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '77' because it was < 2 characters long 743s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '88' because it was < 2 characters long 743s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '96' because it was < 2 characters long 743s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '97' because it was < 2 characters long 743s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '104' because it was < 2 characters long 743s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '105' because it was < 2 characters long 743s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '106' because it was < 2 characters long 743s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '115' because it was < 2 characters long 743s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '122' because it was < 2 characters long 743s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '124' because it was < 2 characters long 743s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '126' because it was < 2 characters long 743s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '131' because it was < 2 characters long 743s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '133' because it was < 2 characters long 743s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '134' because it was < 2 characters long 743s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '144' because it was < 2 characters long 743s Warning: skipping mate #1 of read '149' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '149' because it was < 2 characters long 743s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '152' because it was < 2 characters long 743s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '156' because it was < 2 characters long 743s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '161' because it was < 2 characters long 743s Warning: skipping mate #1 of read '162' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '162' because it was < 2 characters long 743s Warning: skipping mate #1 of read '163' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '163' because it was < 2 characters long 743s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '164' because it was < 2 characters long 743s Read 150 alignments... 743s 174 reads; of these: 743s 145 (83.33%) were paired; of these: 743s 145 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 145 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 145 pairs aligned 0 times concordantly or discordantly; of these: 743s 290 mates make up the pairs; of these: 743s 282 (97.24%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 8 (2.76%) aligned >1 times 743s 29 (16.67%) were unpaired; of these: 743s 29 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 2.51% overall alignment rate 743s Read 200 alignments... 743s Read 250 alignments... 743s Read 300 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s 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ACACCTG 743s Processing line... 743s ACACCTG 743s ACACCTG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TCAAC 743s TCAAC 743s Processing line... 743s TCAAC 743s TCAAC 743s Processing line... 743s Processing line... 743s TTGGCGTCAAC 743s TTGGCGTCAAC 743s Processing line... 743s TTGGCGTCAAC 743s TTGGCGTCAAC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGCGTCAACAC 743s TGGCGTCAACAC 743s Processing line... 743s TGGCGTCAACAC 743s TGGCGTCAACAC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGCGTCAACA 743s TGGCGTCAACA 743s Processing line... 743s TGGCGTCAACA 743s TGGCGTCAACA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CGTCAACACCTG 743s CGTCAACACCTG 743s Processing line... 743s CGTCAACACCTG 743s CGTCAACACCTG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GCGTC 743s GCGTC 743s Processing line... 743s GCGTC 743s GCGTC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 16 alignments, 0 edits 743s --------------- 743s PASSED 743s ALSO checking that bowtie2 and bowtie2-align match up 743s /usr/bin/bowtie2 --trim5 4 --np 6 --cp-min 6 --mm -a --score-min L,3.65754688293277,1.39494813493015 --gbar 7 --trim3 6 --cp-ival 1 --local -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 743s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '2' because it was < 2 characters long 743s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '3' because it was < 2 characters long 743s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '8' because it was < 2 characters long 743s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '14' because it was < 2 characters long 743s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '15' because it was < 2 characters long 743s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '20' because it was < 2 characters long 743s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '26' because it was < 2 characters long 743s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '27' because it was < 2 characters long 743s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '28' because it was < 2 characters long 743s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '31' because it was < 2 characters long 743s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '38' because it was < 2 characters long 743s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '39' because it was < 2 characters long 743s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '44' because it was < 2 characters long 743s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '48' because it was < 2 characters long 743s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '53' because it was < 2 characters long 743s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '58' because it was < 2 characters long 743s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '62' because it was < 2 characters long 743s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '71' because it was < 2 characters long 743s Warning: skipping mate #2 of read '71' because it was < 2 characters long 743s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '74' because it was < 2 characters long 743s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '76' because it was < 2 characters long 743s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '77' because it was < 2 characters long 743s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '88' because it was < 2 characters long 743s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '96' because it was < 2 characters long 743s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '97' because it was < 2 characters long 743s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '104' because it was < 2 characters long 743s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '105' because it was < 2 characters long 743s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '106' because it was < 2 characters long 743s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '115' because it was < 2 characters long 743s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '122' because it was < 2 characters long 743s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '124' because it was < 2 characters long 743s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '126' because it was < 2 characters long 743s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '131' because it was < 2 characters long 743s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '133' because it was < 2 characters long 743s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '134' because it was < 2 characters long 743s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '144' because it was < 2 characters long 743s Warning: skipping mate #1 of read '149' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '149' because it was < 2 characters long 743s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '152' because it was < 2 characters long 743s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '156' because it was < 2 characters long 743s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '161' because it was < 2 characters long 743s Warning: skipping mate #1 of read '162' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '162' because it was < 2 characters long 743s Warning: skipping mate #1 of read '163' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '163' because it was < 2 characters long 743s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '164' because it was < 2 characters long 743s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 743s 174 reads; of these: 743s 145 (83.33%) were paired; of these: 743s 145 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 145 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 145 pairs aligned 0 times concordantly or discordantly; of these: 743s 290 mates make up the pairs; of these: 743s 282 (97.24%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 8 (2.76%) aligned >1 times 743s 29 (16.67%) were unpaired; of these: 743s 29 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 2.51% overall alignment rate 743s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 743s /usr/bin/bowtie2 --trim5 4 --np 6 --cp-min 6 --mm -a --score-min L,3.65754688293277,1.39494813493015 --gbar 7 --trim3 6 --cp-ival 1 --local -q -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 743s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '2' because it was < 2 characters long 743s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '3' because it was < 2 characters long 743s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '8' because it was < 2 characters long 743s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '14' because it was < 2 characters long 743s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '15' because it was < 2 characters long 743s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '20' because it was < 2 characters long 743s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '26' because it was < 2 characters long 743s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '27' because it was < 2 characters long 743s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '28' because it was < 2 characters long 743s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '31' because it was < 2 characters long 743s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '38' because it was < 2 characters long 743s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '39' because it was < 2 characters long 743s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '44' because it was < 2 characters long 743s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '48' because it was < 2 characters long 743s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '53' because it was < 2 characters long 743s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '58' because it was < 2 characters long 743s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '62' because it was < 2 characters long 743s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '71' because it was < 2 characters long 743s Warning: skipping mate #2 of read '71' because it was < 2 characters long 743s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '74' because it was < 2 characters long 743s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '76' because it was < 2 characters long 743s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '77' because it was < 2 characters long 743s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '88' because it was < 2 characters long 743s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '96' because it was < 2 characters long 743s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '97' because it was < 2 characters long 743s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '104' because it was < 2 characters long 743s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '105' because it was < 2 characters long 743s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '106' because it was < 2 characters long 743s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '115' because it was < 2 characters long 743s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '122' because it was < 2 characters long 743s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '124' because it was < 2 characters long 743s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '126' because it was < 2 characters long 743s Warning: skipping mate #1 of read '131' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '131' because it was < 2 characters long 743s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '133' because it was < 2 characters long 743s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '134' because it was < 2 characters long 743s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '144' because it was < 2 characters long 743s Warning: skipping mate #1 of read '149' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '149' because it was < 2 characters long 743s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '152' because it was < 2 characters long 743s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '156' because it was < 2 characters long 743s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '161' because it was < 2 characters long 743s Warning: skipping mate #1 of read '162' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '162' because it was < 2 characters long 743s Warning: skipping mate #1 of read '163' because length (1) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '163' because it was < 2 characters long 743s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (0) 743s Warning: skipping mate #1 of read '164' because it was < 2 characters long 743s 174 reads; of these: 743s 145 (83.33%) were paired; of these: 743s 145 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 145 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 145 pairs aligned 0 times concordantly or discordantly; of these: 743s 290 mates make up the pairs; of these: 743s 282 (97.24%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 8 (2.76%) aligned >1 times 743s 29 (16.67%) were unpaired; of these: 743s 29 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 2.51% overall alignment rate 743s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.2 743s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.1 743s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 7 743s Reference gaps introduced: 1 743s Read gaps introduced: 1 743s Rearrangements introduced: 0 743s Created read sampler 743s Sampling 175 reads 743s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 743s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 94 reference bases 743s *** Run 49 of 100 743s /usr/bin/bowtie2 --trim3 3 -D 44 --cp-ival 4 --local --n-ceil 1.40861874177707,0.365882759261893 --gbar 6 --rfg 19.4387616125377,8.06877320252626 --rdg 2.82802816218808,17.3381721888411 --score-min L,2.52225010580908,5.42874082198505 --cp-min 14 --trim5 6 --np 1 -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta 743s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '1' because it was < 2 characters long 743s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '2' because it was < 2 characters long 743s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '3' because it was < 2 characters long 743s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '8' because it was < 2 characters long 743s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '14' because it was < 2 characters long 743s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '21' because it was < 2 characters long 743s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '22' because it was < 2 characters long 743s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '27' because it was < 2 characters long 743s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '30' because it was < 2 characters long 743s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '31' because it was < 2 characters long 743s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '36' because it was < 2 characters long 743s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '39' because it was < 2 characters long 743s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '41' because it was < 2 characters long 743s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '44' because it was < 2 characters long 743s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '53' because it was < 2 characters long 743s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '55' because it was < 2 characters long 743s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '56' because it was < 2 characters long 743s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '63' because it was < 2 characters long 743s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '66' because it was < 2 characters long 743s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '73' because it was < 2 characters long 743s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '76' because it was < 2 characters long 743s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '78' because it was < 2 characters long 743s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '80' because it was < 2 characters long 743s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '82' because it was < 2 characters long 743s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '83' because it was < 2 characters long 743s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '86' because it was < 2 characters long 743s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '89' because it was < 2 characters long 743s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '92' because it was < 2 characters long 743s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '96' because it was < 2 characters long 743s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '102' because it was < 2 characters long 743s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '103' because it was < 2 characters long 743s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '104' because it was < 2 characters long 743s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '105' because it was < 2 characters long 743s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '109' because it was < 2 characters long 743s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '110' because it was < 2 characters long 743s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '115' because it was < 2 characters long 743s Warning: skipping read '116' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '116' because it was < 2 characters long 743s Warning: skipping read '121' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '121' because it was < 2 characters long 743s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '122' because it was < 2 characters long 743s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '128' because it was < 2 characters long 743s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '131' because it was < 2 characters long 743s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '134' because it was < 2 characters long 743s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '135' because it was < 2 characters long 743s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '136' because it was < 2 characters long 743s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '137' because it was < 2 characters long 743s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '141' because it was < 2 characters long 743s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '143' because it was < 2 characters long 743s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '144' because it was < 2 characters long 743s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '146' because it was < 2 characters long 743s Warning: skipping read '150' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '150' because it was < 2 characters long 743s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '152' because it was < 2 characters long 743s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '153' because it was < 2 characters long 743s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '159' because it was < 2 characters long 743s Warning: skipping read '163' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '163' because it was < 2 characters long 743s Warning: skipping read '171' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '171' because it was < 2 characters long 743s Warning: skipping read '173' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '173' because it was < 2 characters long 743s Warning: skipping read '174' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '174' because it was < 2 characters long 743s Warning: skipping read '175' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '175' because it was < 2 characters long 743s 175 reads; of these: 743s 175 (100.00%) were unpaired; of these: 743s 175 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s Read 50 alignments... 743s Read 100 alignments... 743s Read 150 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 0 alignments, 0 edits 743s --------------- 743s PASSED 743s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 743s /usr/bin/bowtie2 --trim3 3 -D 44 --cp-ival 4 --local --n-ceil 1.40861874177707,0.365882759261893 --gbar 6 --rfg 19.4387616125377,8.06877320252626 --rdg 2.82802816218808,17.3381721888411 --score-min L,2.52225010580908,5.42874082198505 --cp-min 14 --trim5 6 --np 1 -f -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 743s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '1' because it was < 2 characters long 743s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '2' because it was < 2 characters long 743s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '3' because it was < 2 characters long 743s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '8' because it was < 2 characters long 743s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '14' because it was < 2 characters long 743s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '21' because it was < 2 characters long 743s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '22' because it was < 2 characters long 743s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '27' because it was < 2 characters long 743s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '30' because it was < 2 characters long 743s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '31' because it was < 2 characters long 743s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '36' because it was < 2 characters long 743s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '39' because it was < 2 characters long 743s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '41' because it was < 2 characters long 743s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '44' because it was < 2 characters long 743s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '53' because it was < 2 characters long 743s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '55' because it was < 2 characters long 743s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '56' because it was < 2 characters long 743s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '63' because it was < 2 characters long 743s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '66' because it was < 2 characters long 743s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '73' because it was < 2 characters long 743s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '76' because it was < 2 characters long 743s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '78' because it was < 2 characters long 743s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '80' because it was < 2 characters long 743s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '82' because it was < 2 characters long 743s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '83' because it was < 2 characters long 743s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '86' because it was < 2 characters long 743s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '89' because it was < 2 characters long 743s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '92' because it was < 2 characters long 743s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '96' because it was < 2 characters long 743s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '102' because it was < 2 characters long 743s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '103' because it was < 2 characters long 743s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '104' because it was < 2 characters long 743s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '105' because it was < 2 characters long 743s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '109' because it was < 2 characters long 743s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '110' because it was < 2 characters long 743s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '115' because it was < 2 characters long 743s Warning: skipping read '116' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '116' because it was < 2 characters long 743s Warning: skipping read '121' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '121' because it was < 2 characters long 743s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '122' because it was < 2 characters long 743s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '128' because it was < 2 characters long 743s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '131' because it was < 2 characters long 743s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '134' because it was < 2 characters long 743s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '135' because it was < 2 characters long 743s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '136' because it was < 2 characters long 743s Warning: skipping read '137' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '137' because it was < 2 characters long 743s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '141' because it was < 2 characters long 743s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '143' because it was < 2 characters long 743s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '144' because it was < 2 characters long 743s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '146' because it was < 2 characters long 743s Warning: skipping read '150' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '150' because it was < 2 characters long 743s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '152' because it was < 2 characters long 743s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '153' because it was < 2 characters long 743s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '159' because it was < 2 characters long 743s Warning: skipping read '163' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '163' because it was < 2 characters long 743s Warning: skipping read '171' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '171' because it was < 2 characters long 743s Warning: skipping read '173' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '173' because it was < 2 characters long 743s Warning: skipping read '174' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '174' because it was < 2 characters long 743s Warning: skipping read '175' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '175' because it was < 2 characters long 743s 175 reads; of these: 743s 175 (100.00%) were unpaired; of these: 743s 175 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.2 743s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.1 743s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 7 743s Reference gaps introduced: 0 743s Read gaps introduced: 0 743s Rearrangements introduced: 0 743s Created read sampler 743s Sampling 67 reads 743s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 743s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 94 reference bases 743s *** Run 50 of 100 743s /usr/bin/bowtie2 --cp-min 15 --cp-ival 2 --local --mp 5.6620080439703,3.91343206383368 --score-min L,1.73831792909513,3.66394810911063 --rdg 8.13185575055319,9.48441539666397 -i S,0.80337638514442 --trim5 5 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 743s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '2' because it was < 2 characters long 743s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '4' because it was < 2 characters long 743s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '9' because it was < 2 characters long 743s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '10' because it was < 2 characters long 743s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '14' because it was < 2 characters long 743s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '15' because it was < 2 characters long 743s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '16' because it was < 2 characters long 743s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '17' because it was < 2 characters long 743s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '25' because it was < 2 characters long 743s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '26' because it was < 2 characters long 743s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '34' because it was < 2 characters long 743s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '43' because it was < 2 characters long 743s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 743s Warning: skipping read '53' because it was < 2 characters long 743s Warning: skipping read '61' because length (1) <= # seed mismatches (0) 743s Warning: skipping read '61' because it was < 2 characters long 743s 67 reads; of these: 743s 67 (100.00%) were unpaired; of these: 743s 67 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 0.00% overall alignment rate 743s Read 50 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 0 alignments, 0 edits 743s --------------- 743s PASSED 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.2 743s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.1 743s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 10 743s Reference gaps introduced: 0 743s Read gaps introduced: 1 743s Rearrangements introduced: 1 743s Created read sampler 743s Sampling 86 reads 743s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 743s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 94 reference bases 743s *** Run 51 of 100 743s /usr/bin/bowtie2 --score-min L,5.48573752692327,1.93306776057499 --rfg 8.45368752142575 --mm --trim5 1 -k 4 --mp 9.19577489962842,8.44118586438745 --cp-min 5 --cp-ival 1 --trim3 1 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 743s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 743s 86 reads; of these: 743s 86 (100.00%) were unpaired; of these: 743s 73 (84.88%) aligned 0 times 743s 3 (3.49%) aligned exactly 1 time 743s 10 (11.63%) aligned >1 times 743s 15.12% overall alignment rate 743s Read 50 alignments... 743s Read 100 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GCG 743s GCG 743s Processing line... 743s GCG 743s GCG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TTGGCGTCAA 743s TTGGCGTCAA 743s Processing line... 743s TTGGCGTCAA 743s TTGGCGTCAA 743s Processing line... 743s Processing line... 743s Processing line... 743s TCAA 743s TCAA 743s Processing line... 743s TCAA 743s TCAA 743s Processing line... 743s TCAA 743s TCAA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CACCT 743s CACCT 743s Processing line... 743s CACCT 743s CACCT 743s Processing line... 743s Processing line... 743s Processing line... 743s TA 743s TA 743s Processing line... 743s TA 743s TA 743s Processing line... 743s TA 743s TA 743s Processing line... 743s TA 743s TA 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGATTCAATCAT 743s TGGATTCAATCAT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TCAATCAT 743s TCAATCAT 743s Processing line... 743s CAACACC 743s CAACACC 743s Processing line... 743s CAACACC 743s CAACACC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GTCAACACCTG 743s GTCAACACCTG 743s Processing line... 743s GTCAACACCTG 743s GTCAACACCTG 743s Processing line... 743s Processing line... 743s GGCGT 743s GGCGT 743s Processing line... 743s GGCGT 743s GGCGT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CGTC 743s CGTC 743s Processing line... 743s CGTC 743s CGTC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s AAA 743s AAA 743s Processing line... 743s AAA 743s AAA 743s Processing line... 743s TTT 743s TTT 743s Processing line... 743s Processing line... 743s Processing line... 743s CATGGATTCAATCATA 743s CATGGATTCAATCATA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 27 alignments, 0 edits 743s --------------- 743s PASSED 743s Flattened IUPAC characters 743s Mutating sequence Sim.pm.2 743s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutating sequence Sim.pm.1 743s Introducing 5 SNPs, 0/2 ref/read gaps, and 0 rearrangements 743s Finished SNPs 743s Finished ref gaps 743s Finished read gaps 743s Mutated reference genome to subject genome 743s SNPs introduced: 8 743s Reference gaps introduced: 0 743s Read gaps introduced: 2 743s Rearrangements introduced: 0 743s Created read sampler 743s Sampling 166 reads 743s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 743s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 743s parsing sequence Sim.pm.1... 743s parsing sequence Sim.pm.2... 743s Parsed 94 reference bases 743s *** Run 52 of 100 743s /usr/bin/bowtie2 --trim5 6 -i C,3.81046765665047 -M 6 --gbar 4 --np 2 --rfg 48.5516975689187,2.24715327518435 --score-min L,8.3923671228584,9.14772315675228 --cp-ival 1 --cp-min 3 -N 1 -L13 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 743s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 743s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 743s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 743s Warning: skipping mate #2 of read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #2 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 743s Read 50 alignments... 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 743s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 743s Read 100 alignments... 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 743s Read 150 alignments... 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 743s Read 200 alignments... 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 743s Read 250 alignments... 743s 166 reads; of these: 743s 149 (89.76%) were paired; of these: 743s 149 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 149 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 149 pairs aligned 0 times concordantly or discordantly; of these: 743s 298 mates make up the pairs; of these: 743s 275 (92.28%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 23 (7.72%) aligned >1 times 743s 17 (10.24%) were unpaired; of these: 743s 17 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 7.30% overall alignment rate 743s Read 300 alignments... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TT 743s TT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GCGTC 743s GCGTC 743s Processing line... 743s Processing line... 743s TTGGCGTCAACACCTG 743s TTGGCGTCAACACCTG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGCGTCAACACC 743s TGGCGTCAACACC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s ACAT 743s ACAT 743s Processing line... 743s Processing line... 743s GGCGTCAACACCTG 743s GGCGTCAACACCTG 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s ACAT 743s ACAT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s ACA 743s ACA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TCA 743s TCA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s AC 743s AC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CA 743s CA 743s Processing line... 743s Processing line... 743s GGCGTCAA 743s GGCGTCAA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CAACA 743s CAACA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CAACA 743s CAACA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CC 743s CC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GA 743s GA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CAACACCT 743s CAACACCT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TGGCGTC 743s TGGCGTC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s CA 743s CA 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s ACAC 743s ACAC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s TTGGCG 743s TTGGCG 743s Processing line... 743s Processing line... 743s AACACCT 743s AACACCT 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s GCGTCAACAC 743s GCGTCAACAC 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s Processing line... 743s --- Summary --- 743s Read 1 reference strings 743s Checked 23 alignments, 0 edits 743s --------------- 743s PASSED 743s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 743s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 743s /usr/bin/bowtie2 --trim5 6 -i C,3.81046765665047 -M 6 --gbar 4 --np 2 --rfg 48.5516975689187,2.24715327518435 --score-min L,8.3923671228584,9.14772315675228 --cp-ival 1 --cp-min 3 -N 1 -L13 --qseq -p 2 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 743s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 743s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 743s Warning: skipping mate #2 of read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #2 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 743s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 743s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because length (1) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 743s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (1) 743s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 743s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 743s 166 reads; of these: 743s 149 (89.76%) were paired; of these: 743s 149 (100.00%) aligned concordantly 0 times 743s 0 (0.00%) aligned concordantly exactly 1 time 743s 0 (0.00%) aligned concordantly >1 times 743s ---- 743s 149 pairs aligned concordantly 0 times; of these: 743s 0 (0.00%) aligned discordantly 1 time 743s ---- 743s 149 pairs aligned 0 times concordantly or discordantly; of these: 743s 298 mates make up the pairs; of these: 743s 275 (92.28%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 23 (7.72%) aligned >1 times 743s 17 (10.24%) were unpaired; of these: 743s 17 (100.00%) aligned 0 times 743s 0 (0.00%) aligned exactly 1 time 743s 0 (0.00%) aligned >1 times 743s 7.30% overall alignment rate 743s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 743s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 743s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 743s /usr/bin/bowtie2 --trim5 6 -i C,3.81046765665047 -M 6 --gbar 4 --np 2 --rfg 48.5516975689187,2.24715327518435 --score-min L,8.3923671228584,9.14772315675228 --cp-ival 1 --cp-min 3 -N 1 -L13 --qseq -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 743s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 744s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (1) 744s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 744s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 744s Warning: skipping mate #2 of read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (1) 744s Warning: skipping mate #2 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (1) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 744s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (1) 744s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 744s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_152_152_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_157_157_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because length (1) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 744s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (1) 744s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 744s 166 reads; of these: 744s 149 (89.76%) were paired; of these: 744s 149 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 149 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 149 pairs aligned 0 times concordantly or discordantly; of these: 744s 298 mates make up the pairs; of these: 744s 275 (92.28%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 23 (7.72%) aligned >1 times 744s 17 (10.24%) were unpaired; of these: 744s 17 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 7.30% overall alignment rate 744s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.1 744s Introducing 6 SNPs, 0/2 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.2 744s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 11 744s Reference gaps introduced: 0 744s Read gaps introduced: 2 744s Rearrangements introduced: 0 744s Created read sampler 744s Sampling 28 reads 744s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 744s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 94 reference bases 744s *** Run 53 of 100 744s /usr/bin/bowtie2 --trim3 5 --mp 7.02007543142252,4.99446551666109 --cp-ival 2 --local --mm --score-min L,2.99874931289521,4.63091077871035 --cp-min 2 --trim5 2 -M 5 --np 1 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '6' because it was < 2 characters long 744s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '11' because it was < 2 characters long 744s 28 reads; of these: 744s 23 (82.14%) were paired; of these: 744s 23 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 23 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 23 pairs aligned 0 times concordantly or discordantly; of these: 744s 46 mates make up the pairs; of these: 744s 46 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 5 (17.86%) were unpaired; of these: 744s 5 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s Read 50 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 0 alignments, 0 edits 744s --------------- 744s PASSED 744s /usr/bin/bowtie2 --trim3 5 --mp 7.02007543142252,4.99446551666109 --cp-ival 2 --local --mm --score-min L,2.99874931289521,4.63091077871035 --cp-min 2 --trim5 2 -M 5 --np 1 -f -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '6' because it was < 2 characters long 744s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '11' because it was < 2 characters long 744s 28 reads; of these: 744s 23 (82.14%) were paired; of these: 744s 23 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 23 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 23 pairs aligned 0 times concordantly or discordantly; of these: 744s 46 mates make up the pairs; of these: 744s 46 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 5 (17.86%) were unpaired; of these: 744s 5 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.2 744s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.1 744s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 7 744s Reference gaps introduced: 0 744s Read gaps introduced: 0 744s Rearrangements introduced: 1 744s Created read sampler 744s Sampling 140 reads 744s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 744s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 94 reference bases 744s *** Run 54 of 100 744s /usr/bin/bowtie2 --trim5 7 -M 11 --np 7 -R 2 --cp-min 3 --mm --score-min L,8.3708996723995,5.29405602952222 --rdg 34.1399093074223 --cp-ival 2 --local --n-ceil 0.865688984088397,1.09857060428639 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping read '0' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '0' because it was < 2 characters long 744s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '6' because it was < 2 characters long 744s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '10' because it was < 2 characters long 744s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '13' because it was < 2 characters long 744s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '14' because it was < 2 characters long 744s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '16' because it was < 2 characters long 744s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '20' because it was < 2 characters long 744s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '26' because it was < 2 characters long 744s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '29' because it was < 2 characters long 744s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '45' because it was < 2 characters long 744s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '46' because it was < 2 characters long 744s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '49' because it was < 2 characters long 744s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '54' because it was < 2 characters long 744s Warning: skipping mate #2 of read '54' because it was < 2 characters long 744s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '60' because it was < 2 characters long 744s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '61' because it was < 2 characters long 744s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '68' because it was < 2 characters long 744s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '71' because it was < 2 characters long 744s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '75' because it was < 2 characters long 744s /usr/bin/bowtie2 --trim5 7 -M 11 --np 7 -R 2 --cp-min 3 --mm --score-min L,8.3708996723995,5.29405602952222 --rdg 34.1399093074223 --cp-ival 2 --local --n-ceil 0.865688984088397,1.09857060428639 -r -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '81' because it was < 2 characters long 744s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '82' because it was < 2 characters long 744s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '93' because it was < 2 characters long 744s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '96' because it was < 2 characters long 744s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '99' because it was < 2 characters long 744s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '102' because it was < 2 characters long 744s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '105' because it was < 2 characters long 744s Warning: skipping mate #2 of read '121' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '121' because it was < 2 characters long 744s Warning: skipping mate #2 of read '128' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '128' because it was < 2 characters long 744s Read 50 alignments... 744s 140 reads; of these: 744s 120 (85.71%) were paired; of these: 744s 120 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 120 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 120 pairs aligned 0 times concordantly or discordantly; of these: 744s 240 mates make up the pairs; of these: 744s 240 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 20 (14.29%) were unpaired; of these: 744s 20 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s Read 100 alignments... 744s Read 150 alignments... 744s Read 200 alignments... 744s Read 250 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing 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Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing 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Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing 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line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 0 alignments, 0 edits 744s --------------- 744s PASSED 744s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping read '0' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '0' because it was < 2 characters long 744s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '6' because it was < 2 characters long 744s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '10' because it was < 2 characters long 744s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '13' because it was < 2 characters long 744s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '14' because it was < 2 characters long 744s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '16' because it was < 2 characters long 744s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '20' because it was < 2 characters long 744s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '26' because it was < 2 characters long 744s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '29' because it was < 2 characters long 744s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '45' because it was < 2 characters long 744s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '46' because it was < 2 characters long 744s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '49' because it was < 2 characters long 744s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '54' because it was < 2 characters long 744s Warning: skipping mate #2 of read '54' because it was < 2 characters long 744s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '60' because it was < 2 characters long 744s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '61' because it was < 2 characters long 744s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '68' because it was < 2 characters long 744s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '71' because it was < 2 characters long 744s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '75' because it was < 2 characters long 744s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '81' because it was < 2 characters long 744s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '82' because it was < 2 characters long 744s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '93' because it was < 2 characters long 744s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '96' because it was < 2 characters long 744s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '99' because it was < 2 characters long 744s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '102' because it was < 2 characters long 744s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '105' because it was < 2 characters long 744s Warning: skipping mate #2 of read '121' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '121' because it was < 2 characters long 744s Warning: skipping mate #2 of read '128' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '128' because it was < 2 characters long 744s 140 reads; of these: 744s 120 (85.71%) were paired; of these: 744s 120 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 120 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 120 pairs aligned 0 times concordantly or discordantly; of these: 744s 240 mates make up the pairs; of these: 744s 240 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 20 (14.29%) were unpaired; of these: 744s 20 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.1 744s Introducing 7 SNPs, 0/0 ref/read gaps, and 2 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.2 744s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 9 744s Reference gaps introduced: 0 744s Read gaps introduced: 0 744s Rearrangements introduced: 2 744s Created read sampler 744s Sampling 125 reads 744s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 744s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 94 reference bases 744s *** Run 55 of 100 744s /usr/bin/bowtie2 --cp-ival 1 --local --rfg 26.5164690166246,13.014049302877 --rdg 33.4661928031717,15.8124313140552 --score-min L,9.13977359602263,5.73875610939892 --cp-min 5 -k 4 -i L,0.111488249840448 --trim5 3 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 744s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '2' because it was < 2 characters long 744s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '27' because it was < 2 characters long 744s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '30' because it was < 2 characters long 744s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '39' because it was < 2 characters long 744s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '41' because it was < 2 characters long 744s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '44' because it was < 2 characters long 744s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '49' because it was < 2 characters long 744s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '52' because it was < 2 characters long 744s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '54' because it was < 2 characters long 744s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '65' because it was < 2 characters long 744s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '70' because it was < 2 characters long 744s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '82' because it was < 2 characters long 744s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '87' because it was < 2 characters long 744s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '106' because it was < 2 characters long 744s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '108' because it was < 2 characters long 744s Warning: skipping read '113' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '113' because it was < 2 characters long 744s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '116' because it was < 2 characters long 744s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '117' because it was < 2 characters long 744s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '119' because it was < 2 characters long 744s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '120' because it was < 2 characters long 744s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '125' because it was < 2 characters long 744s 125 reads; of these: 744s 125 (100.00%) were unpaired; of these: 744s 125 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s Read 50 alignments... 744s Read 100 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 0 alignments, 0 edits 744s --------------- 744s PASSED 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.1 744s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.2 744s Introducing 2 SNPs, 2/0 ref/read gaps, and 1 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 4 744s Reference gaps introduced: 2 744s Read gaps introduced: 1 744s Rearrangements introduced: 1 744s Created read sampler 744s Sampling 71 reads 744s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 744s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 94 reference bases 744s *** Run 56 of 100 744s /usr/bin/bowtie2 -i S,2.25456214260207 -k 2 --norc --ma 6.22943770256928 --cp-min 2 --score-min L,8.28289270310005,7.51482510183013 --rdg 6.34722727188576 --trim3 9 --mp 6.57579000431213,5.75324087265203 --cp-ival 1 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 744s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 744s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '4' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 744s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '8' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 744s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '21' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 744s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '29' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 744s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '37' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 744s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '38' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 744s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '41' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 744s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '43' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 744s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '44' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 744s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '49' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 744s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '54' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 744s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '55' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 744s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '59' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 744s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '62' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 744s Read 50 alignments... 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 744s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '65' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 744s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '68' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 744s Read 100 alignments... 744s 71 reads; of these: 744s 61 (85.92%) were paired; of these: 744s 61 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 61 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 61 pairs aligned 0 times concordantly or discordantly; of these: 744s 122 mates make up the pairs; of these: 744s 117 (95.90%) aligned 0 times 744s 1 (0.82%) aligned exactly 1 time 744s 4 (3.28%) aligned >1 times 744s 10 (14.08%) were unpaired; of these: 744s 8 (80.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 2 (20.00%) aligned >1 times 744s 5.30% overall alignment rate 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GA 744s GA 744s Processing line... 744s GA 744s GA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TTGGCGTCAACACC 744s TTGGCGTCAACACC 744s Processing line... 744s TTGGCGTCAACACC 744s TTGGCGTCAACACC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CACCT 744s CACCT 744s Processing line... 744s CACCT 744s CACCT 744s Processing line... 744s Processing line... 744s TTGGCGTCAACAC 744s TTGGCGTCAACAC 744s Processing line... 744s TTGGCGTCAACAC 744s TTGGCGTCAACAC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TGGCG 744s TGGCG 744s Processing line... 744s TGGCG 744s TGGCG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TGAACATGG 744s TGAACATGG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TGGCGT 744s TGGCGT 744s Processing line... 744s TGGCGT 744s TGGCGT 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 13 alignments, 0 edits 744s --------------- 744s PASSED 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.2 744s Introducing 4 SNPs, 2/1 ref/read gaps, and 1 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.1 744s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 8 744s Reference gaps introduced: 2 744s Read gaps introduced: 2 744s Rearrangements introduced: 1 744s Created read sampler 744s Sampling 208 reads 744s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 744s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 94 reference bases 744s *** Run 57 of 100 744s /usr/bin/bowtie2 --local --cp-ival 3 --trim3 4 --score-min L,9.26422544636725,3.00740628951673 --rdg 25.7681212333452,4.34434961959241 --gbar 3 --cp-min 7 --norc --np 4 --trim5 0 -M 6 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '1' because it was < 2 characters long 744s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '2' because it was < 2 characters long 744s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '17' because it was < 2 characters long 744s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '24' because it was < 2 characters long 744s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '25' because it was < 2 characters long 744s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '50' because it was < 2 characters long 744s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '53' because it was < 2 characters long 744s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '59' because it was < 2 characters long 744s Read 50 alignments... 744s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '100' because it was < 2 characters long 744s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '122' because it was < 2 characters long 744s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '127' because it was < 2 characters long 744s Warning: skipping mate #1 of read '133' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '133' because it was < 2 characters long 744s Warning: skipping mate #2 of read '136' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '136' because it was < 2 characters long 744s Warning: skipping mate #1 of read '157' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '157' because it was < 2 characters long 744s Read 100 alignments... 744s Read 150 alignments... 744s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '167' because it was < 2 characters long 744s Warning: skipping mate #1 of read '168' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '168' because it was < 2 characters long 744s Warning: skipping mate #1 of read '176' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '176' because it was < 2 characters long 744s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '178' because it was < 2 characters long 744s Warning: skipping mate #2 of read '186' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '186' because it was < 2 characters long 744s Warning: skipping mate #1 of read '195' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '195' because it was < 2 characters long 744s Warning: skipping mate #1 of read '196' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '196' because it was < 2 characters long 744s Warning: skipping mate #1 of read '208' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '208' because it was < 2 characters long 744s Read 200 alignments... 744s Read 250 alignments... 744s 208 reads; of these: 744s 187 (89.90%) were paired; of these: 744s 187 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 187 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 187 pairs aligned 0 times concordantly or discordantly; of these: 744s 374 mates make up the pairs; of these: 744s 374 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 21 (10.10%) were unpaired; of these: 744s 21 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s Read 300 alignments... 744s Read 350 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing 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line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 0 alignments, 0 edits 744s --------------- 744s PASSED 744s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 744s /usr/bin/bowtie2 --local --cp-ival 3 --trim3 4 --score-min L,9.26422544636725,3.00740628951673 --rdg 25.7681212333452,4.34434961959241 --gbar 3 --cp-min 7 --norc --np 4 --trim5 0 -M 6 -q -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 744s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '1' because it was < 2 characters long 744s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '2' because it was < 2 characters long 744s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '17' because it was < 2 characters long 744s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '24' because it was < 2 characters long 744s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '25' because it was < 2 characters long 744s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '50' because it was < 2 characters long 744s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '53' because it was < 2 characters long 744s Warning: skipping mate #2 of read '59' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '59' because it was < 2 characters long 744s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '100' because it was < 2 characters long 744s Warning: skipping mate #1 of read '122' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '122' because it was < 2 characters long 744s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '127' because it was < 2 characters long 744s Warning: skipping mate #1 of read '133' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '133' because it was < 2 characters long 744s Warning: skipping mate #2 of read '136' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '136' because it was < 2 characters long 744s Warning: skipping mate #1 of read '157' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '157' because it was < 2 characters long 744s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '167' because it was < 2 characters long 744s Warning: skipping mate #1 of read '168' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '168' because it was < 2 characters long 744s Warning: skipping mate #1 of read '176' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '176' because it was < 2 characters long 744s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '178' because it was < 2 characters long 744s Warning: skipping mate #2 of read '186' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '186' because it was < 2 characters long 744s Warning: skipping mate #1 of read '195' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '195' because it was < 2 characters long 744s Warning: skipping mate #1 of read '196' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '196' because it was < 2 characters long 744s Warning: skipping mate #1 of read '208' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '208' because it was < 2 characters long 744s 208 reads; of these: 744s 187 (89.90%) were paired; of these: 744s 187 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 187 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 187 pairs aligned 0 times concordantly or discordantly; of these: 744s 374 mates make up the pairs; of these: 744s 374 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 21 (10.10%) were unpaired; of these: 744s 21 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 0.00% overall alignment rate 744s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.1 744s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.2 744s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 9 744s Reference gaps introduced: 0 744s Read gaps introduced: 1 744s Rearrangements introduced: 0 744s Created read sampler 744s Sampling 109 reads 744s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 744s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 94 reference bases 744s *** Run 58 of 100 744s /usr/bin/bowtie2 --cp-min 6 -i C,3.46558177125382 --trim5 1 --norc --local --cp-ival 2 --mp 5.67990704150503,2.90429500856673 --mm --gbar 1 --rfg 4.35435178555544 --rdg 16.7772584506622,14.5842520839821 --score-min L,9.98851963785671,1.16102960551508 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 744s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '8' because it was < 2 characters long 744s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '26' because it was < 2 characters long 744s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '40' because it was < 2 characters long 744s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '42' because it was < 2 characters long 744s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '48' because it was < 2 characters long 744s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '54' because it was < 2 characters long 744s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '65' because it was < 2 characters long 744s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 744s Warning: skipping read '82' because it was < 2 characters long 744s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 744s Warning: skipping read '103' because it was < 2 characters long 744s 109 reads; of these: 744s 109 (100.00%) were unpaired; of these: 744s 107 (98.17%) aligned 0 times 744s 1 (0.92%) aligned exactly 1 time 744s 1 (0.92%) aligned >1 times 744s 1.83% overall alignment rate 744s Read 50 alignments... 744s Read 100 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TGGCGTCAACACCT 744s TGGCGTCAACACCT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TGAACATGGAGTCAATCATAACACATT 744s TGAACATGGATTCAATCATAACACATT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 2 alignments, 0 edits 744s --------------- 744s PASSED 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.1 744s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutating sequence Sim.pm.2 744s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 744s Finished SNPs 744s Finished ref gaps 744s Finished read gaps 744s Mutated reference genome to subject genome 744s SNPs introduced: 8 744s Reference gaps introduced: 0 744s Read gaps introduced: 0 744s Rearrangements introduced: 2 744s Created read sampler 744s Sampling 92 reads 744s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 744s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 744s parsing sequence Sim.pm.1... 744s parsing sequence Sim.pm.2... 744s Parsed 94 reference bases 744s *** Run 59 of 100 744s /usr/bin/bowtie2 -R 2 --ma 32.8766773098696 --cp-min 10 --trim5 4 --np 3 --cp-ival 1 -D 39 -a --rfg 26.7600459221769 --score-min L,7.97485098934841,8.93357964155929 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 744s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 744s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '15' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 744s Read 50 alignments... 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 744s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '60' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 744s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '62' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 744s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '86' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 744s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '89' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 744s Read 100 alignments... 744s 92 reads; of these: 744s 85 (92.39%) were paired; of these: 744s 85 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 85 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 85 pairs aligned 0 times concordantly or discordantly; of these: 744s 170 mates make up the pairs; of these: 744s 153 (90.00%) aligned 0 times 744s 7 (4.12%) aligned exactly 1 time 744s 10 (5.88%) aligned >1 times 744s 7 (7.61%) were unpaired; of these: 744s 7 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 9.60% overall alignment rate 744s Read 150 alignments... 744s Read 200 alignments... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GCT 744s GCT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CATT 744s CATT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s ATA 744s ATA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s TGCT 744s TGCT 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s AAC 744s AAC 744s Processing line... 744s AAC 744s AAC 744s Processing line... 744s AAC 744s AAC 744s Processing line... 744s AAC 744s AAC 744s Processing line... 744s Processing line... 744s ACA 744s ACA 744s Processing line... 744s ACA 744s ACA 744s Processing line... 744s ACA 744s ACA 744s Processing line... 744s ACA 744s ACA 744s Processing line... 744s ACA 744s ACA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GA 744s GA 744s Processing line... 744s TC 744s TC 744s Processing line... 744s GA 744s GA 744s Processing line... 744s TC 744s TC 744s Processing line... 744s GA 744s GA 744s Processing line... 744s TC 744s TC 744s Processing line... 744s TC 744s TC 744s Processing line... 744s GA 744s GA 744s Processing line... 744s Processing line... 744s ACACA 744s ACACA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GAACATGGATTCAATCATAA 744s GAACATGGATTCAATCATAA 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s AC 744s AC 744s Processing line... 744s AC 744s AC 744s Processing line... 744s GT 744s GT 744s Processing line... 744s AC 744s AC 744s Processing line... 744s AC 744s AC 744s Processing line... 744s AC 744s AC 744s Processing line... 744s GT 744s GT 744s Processing line... 744s AC 744s AC 744s Processing line... 744s AC 744s AC 744s Processing line... 744s Processing line... 744s GG 744s GG 744s Processing line... 744s GG 744s GG 744s Processing line... 744s GG 744s GG 744s Processing line... 744s CC 744s CC 744s Processing line... 744s CC 744s CC 744s Processing line... 744s CC 744s CC 744s Processing line... 744s CC 744s CC 744s Processing line... 744s CC 744s CC 744s Processing line... 744s CC 744s CC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s GC 744s GC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s ATAACA 744s ATAACA 744s Processing line... 744s Processing line... 744s TCAAC 744s TCAAC 744s Processing line... 744s TCAAC 744s TCAAC 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CTG 744s CTG 744s Processing line... 744s CTG 744s CTG 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s CG 744s CG 744s Processing line... 744s --- Summary --- 744s Read 1 reference strings 744s Checked 68 alignments, 0 edits 744s --------------- 744s PASSED 744s ALSO checking that bowtie2 and bowtie2-align match up 744s /usr/bin/bowtie2 -R 2 --ma 32.8766773098696 --cp-min 10 --trim5 4 --np 3 --cp-ival 1 -D 39 -a --rfg 26.7600459221769 --score-min L,7.97485098934841,8.93357964155929 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 744s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 744s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '15' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 744s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '60' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 744s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '62' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 744s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '86' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 744s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '89' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 744s 92 reads; of these: 744s 85 (92.39%) were paired; of these: 744s 85 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 85 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 85 pairs aligned 0 times concordantly or discordantly; of these: 744s 170 mates make up the pairs; of these: 744s 153 (90.00%) aligned 0 times 744s 7 (4.12%) aligned exactly 1 time 744s 10 (5.88%) aligned >1 times 744s 7 (7.61%) were unpaired; of these: 744s 7 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 9.60% overall alignment rate 744s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 744s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 744s /usr/bin/bowtie2 -R 2 --ma 32.8766773098696 --cp-min 10 --trim5 4 --np 3 --cp-ival 1 -D 39 -a --rfg 26.7600459221769 --score-min L,7.97485098934841,8.93357964155929 -f -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 744s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '15' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 744s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '60' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 744s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '62' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 744s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 744s Warning: skipping mate #2 of read '86' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 744s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 744s Warning: skipping mate #1 of read '89' because it was < 2 characters long 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 744s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 744s 92 reads; of these: 744s 85 (92.39%) were paired; of these: 744s 85 (100.00%) aligned concordantly 0 times 744s 0 (0.00%) aligned concordantly exactly 1 time 744s 0 (0.00%) aligned concordantly >1 times 744s ---- 744s 85 pairs aligned concordantly 0 times; of these: 744s 0 (0.00%) aligned discordantly 1 time 744s ---- 744s 85 pairs aligned 0 times concordantly or discordantly; of these: 744s 170 mates make up the pairs; of these: 744s 153 (90.00%) aligned 0 times 744s 7 (4.12%) aligned exactly 1 time 744s 10 (5.88%) aligned >1 times 744s 7 (7.61%) were unpaired; of these: 744s 7 (100.00%) aligned 0 times 744s 0 (0.00%) aligned exactly 1 time 744s 0 (0.00%) aligned >1 times 744s 9.60% overall alignment rate 744s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 744s Flattened IUPAC characters 744s Mutating sequence Sim.pm.2 744s Introducing 2 SNPs, 0/0 ref/read gaps, and 3 rearrangements 744s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.1 745s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 5 745s Reference gaps introduced: 0 745s Read gaps introduced: 0 745s Rearrangements introduced: 3 745s Created read sampler 745s Sampling 164 reads 745s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 745s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 94 reference bases 745s *** Run 60 of 100 745s /usr/bin/bowtie2 --mm --rfg 36.2493616487811,6.86195048981616 --rdg 40.9381936414849,17.116664777471 --score-min L,2.50791195881205,9.00150652049485 --cp-ival 1 --n-ceil 0.0295632376861177,1.07652415987316 -i L --norc --np 1 --ma 24.5979697503277 --cp-min 3 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 745s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '23' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 745s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '28' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 745s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '31' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 745s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '36' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 745s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '44' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 745s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '60' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 745s Read 50 alignments... 745s Read 100 alignments... 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 745s Warning: skipping mate #1 of read '87' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '87' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 745s Read 150 alignments... 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 745s Warning: skipping mate #2 of read '138' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '138' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 745s Warning: skipping mate #1 of read '144' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '144' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 745s Warning: skipping mate #1 of read '148' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '148' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 745s Read 200 alignments... 745s 164 reads; of these: 745s 164 (100.00%) were paired; of these: 745s 164 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 164 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 164 pairs aligned 0 times concordantly or discordantly; of these: 745s 328 mates make up the pairs; of these: 745s 318 (96.95%) aligned 0 times 745s 3 (0.91%) aligned exactly 1 time 745s 7 (2.13%) aligned >1 times 745s 3.05% overall alignment rate 745s Read 250 alignments... 745s Read 300 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CAACACCTG 745s CAACACCTG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s AT 745s AT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TG 745s TG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TAACACAT 745s TAACACAT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GAT 745s GAT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GTCA 745s GTCA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TGA 745s TGA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GTCA 745s GTCA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CA 745s CA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s /usr/bin/bowtie2 --mm --rfg 36.2493616487811,6.86195048981616 --rdg 40.9381936414849,17.116664777471 --score-min L,2.50791195881205,9.00150652049485 --cp-ival 1 --n-ceil 0.0295632376861177,1.07652415987316 -i L --norc --np 1 --ma 24.5979697503277 --cp-min 3 -f -p 2 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 745s Processing line... 745s AA 745s AA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 10 alignments, 0 edits 745s --------------- 745s PASSED 745s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 745s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '23' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 745s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '28' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 745s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '31' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 745s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '36' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 745s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '44' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 745s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '60' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 745s Warning: skipping mate #1 of read '87' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '87' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 745s Warning: skipping mate #2 of read '138' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '138' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 745s Warning: skipping mate #1 of read '144' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '144' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 745s Warning: skipping mate #1 of read '148' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '148' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 745s 164 reads; of these: 745s 164 (100.00%) were paired; of these: 745s 164 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 164 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 164 pairs aligned 0 times concordantly or discordantly; of these: 745s 328 mates make up the pairs; of these: 745s 318 (96.95%) aligned 0 times 745s 3 (0.91%) aligned exactly 1 time 745s 7 (2.13%) aligned >1 times 745s 3.05% overall alignment rate 745s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 745s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 745s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 745s /usr/bin/bowtie2 --mm --rfg 36.2493616487811,6.86195048981616 --rdg 40.9381936414849,17.116664777471 --score-min L,2.50791195881205,9.00150652049485 --cp-ival 1 --n-ceil 0.0295632376861177,1.07652415987316 -i L --norc --np 1 --ma 24.5979697503277 --cp-min 3 -f -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 745s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 745s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 745s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '23' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 745s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '28' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 745s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '31' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 745s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '36' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 745s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '44' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 745s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '60' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 745s Warning: skipping mate #1 of read '87' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '87' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 745s Warning: skipping mate #2 of read '138' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '138' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 745s Warning: skipping mate #1 of read '144' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '144' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 745s Warning: skipping mate #1 of read '148' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '148' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 745s 164 reads; of these: 745s 164 (100.00%) were paired; of these: 745s 164 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 164 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 164 pairs aligned 0 times concordantly or discordantly; of these: 745s 328 mates make up the pairs; of these: 745s 318 (96.95%) aligned 0 times 745s 3 (0.91%) aligned exactly 1 time 745s 7 (2.13%) aligned >1 times 745s 3.05% overall alignment rate 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.1 745s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.2 745s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 1 745s Reference gaps introduced: 1 745s Read gaps introduced: 1 745s Rearrangements introduced: 0 745s Created read sampler 745s Sampling 84 reads 745s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 745s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 94 reference bases 745s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 745s *** Run 61 of 100 745s /usr/bin/bowtie2 --nofw --mp 8.15269060711316,7.71767841931557 --local --cp-ival 2 --mm --score-min L,6.44889523561862,4.40956556974588 --rdg 2.51910038624123,2.75616503892188 --cp-min 7 --trim5 8 --norc --np 3 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 745s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '2' because it was < 2 characters long 745s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '8' because it was < 2 characters long 745s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '10' because it was < 2 characters long 745s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '11' because it was < 2 characters long 745s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '16' because it was < 2 characters long 745s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '20' because it was < 2 characters long 745s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '25' because it was < 2 characters long 745s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '26' because it was < 2 characters long 745s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '30' because it was < 2 characters long 745s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '31' because it was < 2 characters long 745s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '32' because it was < 2 characters long 745s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '37' because it was < 2 characters long 745s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '44' because it was < 2 characters long 745s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '45' because it was < 2 characters long 745s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '47' because it was < 2 characters long 745s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '49' because it was < 2 characters long 745s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '57' because it was < 2 characters long 745s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '59' because it was < 2 characters long 745s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '61' because it was < 2 characters long 745s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '62' because it was < 2 characters long 745s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '67' because it was < 2 characters long 745s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '69' because it was < 2 characters long 745s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '75' because it was < 2 characters long 745s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '76' because it was < 2 characters long 745s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '77' because it was < 2 characters long 745s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '79' because it was < 2 characters long 745s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '81' because it was < 2 characters long 745s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '83' because it was < 2 characters long 745s 84 reads; of these: 745s 84 (100.00%) were unpaired; of these: 745s 84 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s Read 50 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 0 alignments, 0 edits 745s --------------- 745s PASSED 745s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 745s /usr/bin/bowtie2 --nofw --mp 8.15269060711316,7.71767841931557 --local --cp-ival 2 --mm --score-min L,6.44889523561862,4.40956556974588 --rdg 2.51910038624123,2.75616503892188 --cp-min 7 --trim5 8 --norc --np 3 -q -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 745s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '2' because it was < 2 characters long 745s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '8' because it was < 2 characters long 745s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '10' because it was < 2 characters long 745s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '11' because it was < 2 characters long 745s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '16' because it was < 2 characters long 745s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '20' because it was < 2 characters long 745s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '25' because it was < 2 characters long 745s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '26' because it was < 2 characters long 745s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '30' because it was < 2 characters long 745s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '31' because it was < 2 characters long 745s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '32' because it was < 2 characters long 745s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '37' because it was < 2 characters long 745s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '44' because it was < 2 characters long 745s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '45' because it was < 2 characters long 745s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '47' because it was < 2 characters long 745s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '49' because it was < 2 characters long 745s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '57' because it was < 2 characters long 745s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '59' because it was < 2 characters long 745s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '61' because it was < 2 characters long 745s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '62' because it was < 2 characters long 745s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '67' because it was < 2 characters long 745s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '69' because it was < 2 characters long 745s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '75' because it was < 2 characters long 745s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '76' because it was < 2 characters long 745s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '77' because it was < 2 characters long 745s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '79' because it was < 2 characters long 745s Warning: skipping read '81' because length (1) <= # seed mismatches (0) 745s Warning: skipping read '81' because it was < 2 characters long 745s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '83' because it was < 2 characters long 745s 84 reads; of these: 745s 84 (100.00%) were unpaired; of these: 745s 84 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.2 745s Introducing 6 SNPs, 1/2 ref/read gaps, and 2 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.1 745s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 7 745s Reference gaps introduced: 1 745s Read gaps introduced: 2 745s Rearrangements introduced: 2 745s Created read sampler 745s Sampling 100 reads 745s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 745s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 94 reference bases 745s *** Run 62 of 100 745s /usr/bin/bowtie2 --trim3 8 --mp 9.78434446066119,7.67104669243049 -N 0 -L24 --local --cp-ival 1 --n-ceil 1.3657503233239,0.815194224376003 --mm --score-min L,9.48941230382773,9.2977715676234 --cp-min 3 -i L,0.0691589756768723 --trim5 1 --np 6 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 745s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 745s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 745s Read 50 alignments... 745s Read 100 alignments... 745s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 745s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 745s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 745s 100 reads; of these: 745s 83 (83.00%) were paired; of these: 745s 83 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 83 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 83 pairs aligned 0 times concordantly or discordantly; of these: 745s 166 mates make up the pairs; of these: 745s 166 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 17 (17.00%) were unpaired; of these: 745s 17 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s Read 150 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 0 alignments, 0 edits 745s --------------- 745s PASSED 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.1 745s Introducing 6 SNPs, 2/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.2 745s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 12 745s Reference gaps introduced: 2 745s Read gaps introduced: 0 745s Rearrangements introduced: 0 745s Created read sampler 745s Sampling 114 reads 745s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 745s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 94 reference bases 745s *** Run 63 of 100 745s /usr/bin/bowtie2 --trim3 3 --mp 9.89799629958798,8.35625486927185 -N 1 -L31 --cp-ival 2 --score-min L,5.34664743648145,5.13406574232298 -R 3 --cp-min 18 --trim5 1 -M 6 --np 11 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 745s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 745s Warning: skipping mate #2 of read 'R_1_1_1_45_45_1/1' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #2 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 745s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 745s Warning: skipping mate #2 of read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #2 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 745s Read 50 alignments... 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 745s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 745s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 745s Read 100 alignments... 745s Read 150 alignments... 745s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 745s Read 200 alignments... 745s 114 reads; of these: 745s 105 (92.11%) were paired; of these: 745s 104 (99.05%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 1 (0.95%) aligned concordantly >1 times 745s ---- 745s 104 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 104 pairs aligned 0 times concordantly or discordantly; of these: 745s 208 mates make up the pairs; of these: 745s 193 (92.79%) aligned 0 times 745s 2 (0.96%) aligned exactly 1 time 745s 13 (6.25%) aligned >1 times 745s 9 (7.89%) were unpaired; of these: 745s 8 (88.89%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 1 (11.11%) aligned >1 times 745s 8.22% overall alignment rate 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CGA 745s CGA 745s Processing line... 745s Processing line... 745s CGT 745s CGT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TCA 745s TCA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GGCGT 745s GGCGT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CGAA 745s CGAA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s AACACAT 745s AACACAT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s ACA 745s ACA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GGCGTC 745s GGCGTC 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s AAA 745s AAA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TTGG 745s TTGG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GCGTCA 745s GCGTCA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CATGAACA 745s CATGAACA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s AACAC 745s AACAC 745s Processing line... 745s TT 745s TT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CGTCAACA 745s CGTCAACA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TTGG 745s TTGG 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TT 745s TT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CGTCAA 745s CGTCAA 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 18 alignments, 0 edits 745s --------------- 745s PASSED 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.1 745s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.2 745s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 3 745s Reference gaps introduced: 0 745s Read gaps introduced: 1 745s Rearrangements introduced: 0 745s Created read sampler 745s Sampling 130 reads 745s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 745s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 94 reference bases 745s *** Run 64 of 100 745s /usr/bin/bowtie2 --n-ceil 0.71276203057951,0.269455287793511 --cp-ival 1 --local --cp-min 2 --trim5 5 --np 3 --rdg 36.1739344530666,9.10771131150213 --score-min L,3.20429337647042,4.97115063180579 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 745s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '7' because it was < 2 characters long 745s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '13' because it was < 2 characters long 745s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '21' because it was < 2 characters long 745s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '25' because it was < 2 characters long 745s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '44' because it was < 2 characters long 745s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '56' because it was < 2 characters long 745s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '60' because it was < 2 characters long 745s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '64' because it was < 2 characters long 745s Read 50 alignments... 745s Read 100 alignments... 745s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '66' because it was < 2 characters long 745s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '69' because it was < 2 characters long 745s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '80' because it was < 2 characters long 745s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '82' because it was < 2 characters long 745s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '83' because it was < 2 characters long 745s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '85' because it was < 2 characters long 745s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '95' because it was < 2 characters long 745s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '96' because it was < 2 characters long 745s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '105' because it was < 2 characters long 745s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '110' because it was < 2 characters long 745s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '116' because it was < 2 characters long 745s Read 150 alignments... 745s Read 200 alignments... 745s 130 reads; of these: 745s 120 (92.31%) were paired; of these: 745s 120 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 120 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 120 pairs aligned 0 times concordantly or discordantly; of these: 745s 240 mates make up the pairs; of these: 745s 240 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 10 (7.69%) were unpaired; of these: 745s 10 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s Read 250 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s 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Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 0 alignments, 0 edits 745s --------------- 745s PASSED 745s ALSO checking that bowtie2 and bowtie2-align match up 745s /usr/bin/bowtie2 --n-ceil 0.71276203057951,0.269455287793511 --cp-ival 1 --local --cp-min 2 --trim5 5 --np 3 --rdg 36.1739344530666,9.10771131150213 --score-min L,3.20429337647042,4.97115063180579 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 745s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '7' because it was < 2 characters long 745s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '13' because it was < 2 characters long 745s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '21' because it was < 2 characters long 745s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '25' because it was < 2 characters long 745s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '44' because it was < 2 characters long 745s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '56' because it was < 2 characters long 745s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '60' because it was < 2 characters long 745s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '64' because it was < 2 characters long 745s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '66' because it was < 2 characters long 745s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '69' because it was < 2 characters long 745s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '80' because it was < 2 characters long 745s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '82' because it was < 2 characters long 745s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '83' because it was < 2 characters long 745s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '85' because it was < 2 characters long 745s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '95' because it was < 2 characters long 745s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '96' because it was < 2 characters long 745s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '105' because it was < 2 characters long 745s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '110' because it was < 2 characters long 745s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '116' because it was < 2 characters long 745s 130 reads; of these: 745s 120 (92.31%) were paired; of these: 745s 120 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 120 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 120 pairs aligned 0 times concordantly or discordantly; of these: 745s 240 mates make up the pairs; of these: 745s 240 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 10 (7.69%) were unpaired; of these: 745s 10 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 745s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 745s /usr/bin/bowtie2 --n-ceil 0.71276203057951,0.269455287793511 --cp-ival 1 --local --cp-min 2 --trim5 5 --np 3 --rdg 36.1739344530666,9.10771131150213 --score-min L,3.20429337647042,4.97115063180579 -f -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 745s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '7' because it was < 2 characters long 745s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '13' because it was < 2 characters long 745s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '21' because it was < 2 characters long 745s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '25' because it was < 2 characters long 745s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '44' because it was < 2 characters long 745s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 745s Warning: skipping read '56' because it was < 2 characters long 745s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '60' because it was < 2 characters long 745s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '64' because it was < 2 characters long 745s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '66' because it was < 2 characters long 745s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '69' because it was < 2 characters long 745s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '80' because it was < 2 characters long 745s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '82' because it was < 2 characters long 745s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '83' because it was < 2 characters long 745s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '85' because it was < 2 characters long 745s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '95' because it was < 2 characters long 745s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '96' because it was < 2 characters long 745s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #2 of read '105' because it was < 2 characters long 745s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '110' because it was < 2 characters long 745s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '116' because it was < 2 characters long 745s 130 reads; of these: 745s 120 (92.31%) were paired; of these: 745s 120 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 120 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 120 pairs aligned 0 times concordantly or discordantly; of these: 745s 240 mates make up the pairs; of these: 745s 240 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 10 (7.69%) were unpaired; of these: 745s 10 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 0.00% overall alignment rate 745s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.1 745s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.2 745s Introducing 0 SNPs, 1/1 ref/read gaps, and 2 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 0 745s Reference gaps introduced: 1 745s Read gaps introduced: 1 745s Rearrangements introduced: 3 745s Created read sampler 745s Sampling 43 reads 745s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 745s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 94 reference bases 745s *** Run 65 of 100 745s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 -D 13 --trim3 0 --score-min L,8.34376853202485,4.24932649926876 --norc --mm -i L,0.00982051451445731,1.52008912582303 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 745s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '7' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 745s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '34' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 745s 43 reads; of these: 745s 43 (100.00%) were paired; of these: 745s 43 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 43 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 43 pairs aligned 0 times concordantly or discordantly; of these: 745s 86 mates make up the pairs; of these: 745s 82 (95.35%) aligned 0 times 745s 2 (2.33%) aligned exactly 1 time 745s 2 (2.33%) aligned >1 times 745s 4.65% overall alignment rate 745s Read 50 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TT 745s TT 745s Processing line... 745s Processing line... 745s Processing line... 745s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 -D 13 --trim3 0 --score-min L,8.34376853202485,4.24932649926876 --norc --mm -i L,0.00982051451445731,1.52008912582303 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CA 745s CA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TAA 745s TAA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s ATA 745s ATA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 4 alignments, 0 edits 745s --------------- 745s PASSED 745s ALSO checking that bowtie2 and bowtie2-align match up 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 745s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '7' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 745s Warning: skipping mate #1 of read '34' because length (1) <= # seed mismatches (0) 745s Warning: skipping mate #1 of read '34' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 745s 43 reads; of these: 745s 43 (100.00%) were paired; of these: 745s 43 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 43 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 43 pairs aligned 0 times concordantly or discordantly; of these: 745s 86 mates make up the pairs; of these: 745s 82 (95.35%) aligned 0 times 745s 2 (2.33%) aligned exactly 1 time 745s 2 (2.33%) aligned >1 times 745s 4.65% overall alignment rate 745s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 745s Flattened IUPAC characters 745s Mutating sequence Sim.pm.1 745s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutating sequence Sim.pm.2 745s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 745s Finished SNPs 745s Finished ref gaps 745s Finished read gaps 745s Mutated reference genome to subject genome 745s SNPs introduced: 11 745s Reference gaps introduced: 0 745s Read gaps introduced: 0 745s Rearrangements introduced: 0 745s Created read sampler 745s Sampling 96 reads 745s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 745s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 745s parsing sequence Sim.pm.1... 745s parsing sequence Sim.pm.2... 745s Parsed 94 reference bases 745s *** Run 66 of 100 745s /usr/bin/bowtie2 --mp 9.9782540440334,3.6160101547655 -N 1 -L30 --cp-ival 2 --n-ceil 0.747859531812398,0.583131678200417 --cp-min 3 --trim3 3 --score-min L,3.49043892635373,5.36041180027416 --gbar 3 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 745s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '3' because it was < 2 characters long 745s Warning: skipping mate #2 of read '3' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 745s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '10' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 745s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '27' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 745s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #2 of read '42' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 745s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #2 of read '45' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 745s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '46' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 745s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '57' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 745s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #2 of read '60' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 745s Read 50 alignments... 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 745s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '90' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 745s Warning: skipping mate #1 of read '92' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '92' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 745s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '93' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 745s Read 100 alignments... 745s 96 reads; of these: 745s 91 (94.79%) were paired; of these: 745s 91 (100.00%) aligned concordantly 0 times 745s 0 (0.00%) aligned concordantly exactly 1 time 745s 0 (0.00%) aligned concordantly >1 times 745s ---- 745s 91 pairs aligned concordantly 0 times; of these: 745s 0 (0.00%) aligned discordantly 1 time 745s ---- 745s 91 pairs aligned 0 times concordantly or discordantly; of these: 745s 182 mates make up the pairs; of these: 745s 171 (93.96%) aligned 0 times 745s 4 (2.20%) aligned exactly 1 time 745s 7 (3.85%) aligned >1 times 745s 5 (5.21%) were unpaired; of these: 745s 5 (100.00%) aligned 0 times 745s 0 (0.00%) aligned exactly 1 time 745s 0 (0.00%) aligned >1 times 745s 5.88% overall alignment rate 745s Read 150 alignments... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TCA 745s TCA 745s /usr/bin/bowtie2 --mp 9.9782540440334,3.6160101547655 -N 1 -L30 --cp-ival 2 --n-ceil 0.747859531812398,0.583131678200417 --cp-min 3 --trim3 3 --score-min L,3.49043892635373,5.36041180027416 --gbar 3 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GAT 745s GAT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s CATA 745s CATA 745s Processing line... 745s Processing line... 745s AC 745s AC 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s TGC 745s TGC 745s Processing line... 745s Processing line... 745s TGCTA 745s TGCTA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s GAT 745s GAT 745s Processing line... 745s Processing line... 745s CT 745s CT 745s Processing line... 745s Processing line... 745s CGT 745s CGT 745s Processing line... 745s Processing line... 745s TGCTA 745s TGCTA 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s AT 745s AT 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s Processing line... 745s --- Summary --- 745s Read 1 reference strings 745s Checked 11 alignments, 0 edits 745s --------------- 745s PASSED 745s ALSO checking that bowtie2 and bowtie2-align match up 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 745s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '3' because it was < 2 characters long 745s Warning: skipping mate #2 of read '3' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 745s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '10' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 745s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (1) 745s Warning: skipping mate #1 of read '27' because it was < 2 characters long 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 745s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 746s Warning: skipping mate #2 of read '42' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '42' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 746s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '45' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 746s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '46' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 746s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '57' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 746s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '60' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 746s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '90' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 746s Warning: skipping mate #1 of read '92' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '92' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 746s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '93' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 746s 96 reads; of these: 746s 91 (94.79%) were paired; of these: 746s 91 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 91 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 91 pairs aligned 0 times concordantly or discordantly; of these: 746s 182 mates make up the pairs; of these: 746s 171 (93.96%) aligned 0 times 746s 4 (2.20%) aligned exactly 1 time 746s 7 (3.85%) aligned >1 times 746s 5 (5.21%) were unpaired; of these: 746s 5 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 5.88% overall alignment rate 746s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.2 746s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.1 746s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 7 746s Reference gaps introduced: 0 746s Read gaps introduced: 1 746s Rearrangements introduced: 1 746s Created read sampler 746s Sampling 65 reads 746s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 746s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s Parsed 94 reference bases 746s *** Run 67 of 100 746s /usr/bin/bowtie2 --gbar 2 --score-min L,9.38902654129419,5.77079510573185 --rfg 41.5736679028542,8.5429029465405 --cp-min 3 --cp-ival 1 -D 39 --ma 2.31449706141476 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 746s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 746s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 746s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '26' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 746s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '44' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 746s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '54' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 746s 65 reads; of these: 746s 65 (100.00%) were unpaired; of these: 746s 56 (86.15%) aligned 0 times 746s 4 (6.15%) aligned exactly 1 time 746s 5 (7.69%) aligned >1 times 746s 13.85% overall alignment rate 746s Read 50 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GTCAACACC 746s GTCAACACC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s CATGAACATGGA 746s CATGAACATGGA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TC 746s TC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s AC 746s AC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s ATA 746s ATA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GATTCAAT 746s GATTCAAT 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TCAACAC 746s TCAACAC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s ACAT 746s ACAT 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TGAACATG 746s TGAACATG 746s --- Summary --- 746s Read 1 reference strings 746s Checked 9 alignments, 0 edits 746s --------------- 746s PASSED 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.2 746s Introducing 12 SNPs, 0/1 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.1 746s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 14 746s Reference gaps introduced: 0 746s Read gaps introduced: 1 746s Rearrangements introduced: 1 746s Created read sampler 746s Sampling 47 reads 746s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 746s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s *** Run 68 of 100 746s /usr/bin/bowtie2 --score-min L,9.97378602007954,7.49434644776371 --rdg 18.3469966116802,9.26283422314604 --rfg 31.0548829322984 --trim5 1 --ma 16.716140923962 --cp-min 2 --cp-ival 1 -D 20 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 746s Parsed 94 reference bases 746s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 746s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 746s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 746s Warning: skipping read '10' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 746s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '19' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 746s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 746s Warning: skipping read '20' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 746s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '35' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 746s 47 reads; of these: 746s 47 (100.00%) were unpaired; of these: 746s 42 (89.36%) aligned 0 times 746s 3 (6.38%) aligned exactly 1 time 746s 2 (4.26%) aligned >1 times 746s 10.64% overall alignment rate 746s Read 50 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GAACATGGATTCAA 746s GAACATGGATTCAA 746s Processing line... 746s CATGGATTCAATCATAACACATT 746s CATGGATTCAATCATAACACATT 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GGC 746s GGC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TCATAACA 746s TCATAACA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GA 746s GA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 5 alignments, 0 edits 746s --------------- 746s PASSED 746s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 746s /usr/bin/bowtie2 --score-min L,9.97378602007954,7.49434644776371 --rdg 18.3469966116802,9.26283422314604 --rfg 31.0548829322984 --trim5 1 --ma 16.716140923962 --cp-min 2 --cp-ival 1 -D 20 -r -p 4 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 746s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 746s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 746s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 746s Warning: skipping read '10' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 746s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '19' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 746s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 746s Warning: skipping read '20' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 746s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 746s Warning: skipping read '35' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 746s 47 reads; of these: 746s 47 (100.00%) were unpaired; of these: 746s 42 (89.36%) aligned 0 times 746s 3 (6.38%) aligned exactly 1 time 746s 2 (4.26%) aligned >1 times 746s 10.64% overall alignment rate 746s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.1 746s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.2 746s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 3 746s Reference gaps introduced: 0 746s Read gaps introduced: 0 746s Rearrangements introduced: 0 746s Created read sampler 746s Sampling 208 reads 746s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 746s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s Parsed 94 reference bases 746s *** Run 69 of 100 746s /usr/bin/bowtie2 --np 2 --rdg 41.0375060956869,7.10929770967472 --score-min L,9.10484077265089,5.74954665345674 -M 2 --mm --cp-ival 2 --local -D 46 --n-ceil 1.33155837151337,1.04980989137378 --cp-min 8 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 746s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 746s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '6' because it was < 2 characters long 746s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '24' because it was < 2 characters long 746s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '38' because it was < 2 characters long 746s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '48' because it was < 2 characters long 746s Warning: skipping mate #1 of read '57' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '57' because it was < 2 characters long 746s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '61' because it was < 2 characters long 746s Read 50 alignments... 746s Read 100 alignments... 746s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '123' because it was < 2 characters long 746s Warning: skipping mate #1 of read '135' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '135' because it was < 2 characters long 746s Read 150 alignments... 746s Read 200 alignments... 746s Warning: skipping mate #2 of read '188' because length (1) <= # seed mismatches (0) 746s Read 250 alignments... 746s Warning: skipping mate #2 of read '188' because it was < 2 characters long 746s Warning: skipping mate #1 of read '196' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '196' because it was < 2 characters long 746s Warning: skipping mate #1 of read '200' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '200' because it was < 2 characters long 746s Read 300 alignments... 746s 208 reads; of these: 746s 208 (100.00%) were paired; of these: 746s 208 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 208 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 208 pairs aligned 0 times concordantly or discordantly; of these: 746s 416 mates make up the pairs; of these: 746s 416 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s Read 350 alignments... 746s Read 400 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing 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Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 0 alignments, 0 edits 746s --------------- 746s PASSED 746s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 746s /usr/bin/bowtie2 --np 2 --rdg 41.0375060956869,7.10929770967472 --score-min L,9.10484077265089,5.74954665345674 -M 2 --mm --cp-ival 2 --local -D 46 --n-ceil 1.33155837151337,1.04980989137378 --cp-min 8 -q -p 3 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 746s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 746s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '6' because it was < 2 characters long 746s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '24' because it was < 2 characters long 746s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '38' because it was < 2 characters long 746s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '48' because it was < 2 characters long 746s Warning: skipping mate #1 of read '57' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '57' because it was < 2 characters long 746s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '61' because it was < 2 characters long 746s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '123' because it was < 2 characters long 746s Warning: skipping mate #1 of read '135' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '135' because it was < 2 characters long 746s Warning: skipping mate #2 of read '188' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '188' because it was < 2 characters long 746s Warning: skipping mate #1 of read '196' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '196' because it was < 2 characters long 746s Warning: skipping mate #1 of read '200' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '200' because it was < 2 characters long 746s 208 reads; of these: 746s 208 (100.00%) were paired; of these: 746s 208 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 208 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 208 pairs aligned 0 times concordantly or discordantly; of these: 746s 416 mates make up the pairs; of these: 746s 416 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 746s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 746s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 746s /usr/bin/bowtie2 --np 2 --rdg 41.0375060956869,7.10929770967472 --score-min L,9.10484077265089,5.74954665345674 -M 2 --mm --cp-ival 2 --local -D 46 --n-ceil 1.33155837151337,1.04980989137378 --cp-min 8 -q -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 746s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 746s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 746s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '6' because it was < 2 characters long 746s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '24' because it was < 2 characters long 746s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '38' because it was < 2 characters long 746s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '48' because it was < 2 characters long 746s Warning: skipping mate #1 of read '57' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '57' because it was < 2 characters long 746s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '61' because it was < 2 characters long 746s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '123' because it was < 2 characters long 746s Warning: skipping mate #1 of read '135' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '135' because it was < 2 characters long 746s Warning: skipping mate #2 of read '188' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read '188' because it was < 2 characters long 746s Warning: skipping mate #1 of read '196' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '196' because it was < 2 characters long 746s Warning: skipping mate #1 of read '200' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '200' because it was < 2 characters long 746s 208 reads; of these: 746s 208 (100.00%) were paired; of these: 746s 208 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 208 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 208 pairs aligned 0 times concordantly or discordantly; of these: 746s 416 mates make up the pairs; of these: 746s 416 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.2 746s Introducing 5 SNPs, 0/1 ref/read gaps, and 1 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.1 746s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 9 746s Reference gaps introduced: 1 746s Read gaps introduced: 1 746s Rearrangements introduced: 1 746s Created read sampler 746s Sampling 54 reads 746s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 746s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s Parsed 94 reference bases 746s *** Run 70 of 100 746s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --nofw -a -i S,1.91150641836135,2.4845276866969 --mm --trim5 8 --score-min L,7.93810450646043,5.79167039147205 --rfg 9.56589337955273,9.49124236346949 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 746s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 746s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 746s 54 reads; of these: 746s 49 (90.74%) were paired; of these: 746s 49 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 49 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 49 pairs aligned 0 times concordantly or discordantly; of these: 746s 98 mates make up the pairs; of these: 746s 95 (96.94%) aligned 0 times 746s 1 (1.02%) aligned exactly 1 time 746s 2 (2.04%) aligned >1 times 746s 5 (9.26%) were unpaired; of these: 746s 5 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 2.91% overall alignment rate 746s Read 50 alignments... 746s Read 100 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s ATG 746s ATG 746s Processing line... 746s ATG 746s ATG 746s Processing line... 746s ATG 746s ATG 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s TC 746s TC 746s Processing line... 746s TC 746s TC 746s Processing line... 746s TC 746s TC 746s Processing line... 746s TC 746s TC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s ATAACACAT 746s ATAACACAT 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 8 alignments, 0 edits 746s --------------- 746s PASSED 746s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 746s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --nofw -a -i S,1.91150641836135,2.4845276866969 --mm --trim5 8 --score-min L,7.93810450646043,5.79167039147205 --rfg 9.56589337955273,9.49124236346949 --qseq -p 2 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 746s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 746s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 746s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 746s 54 reads; of these: 746s 49 (90.74%) were paired; of these: 746s 49 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 49 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 49 pairs aligned 0 times concordantly or discordantly; of these: 746s 98 mates make up the pairs; of these: 746s 95 (96.94%) aligned 0 times 746s 1 (1.02%) aligned exactly 1 time 746s 2 (2.04%) aligned >1 times 746s 5 (9.26%) were unpaired; of these: 746s 5 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 2.91% overall alignment rate 746s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 746s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 746s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.2 746s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.1 746s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 2 746s Reference gaps introduced: 1 746s Read gaps introduced: 0 746s Rearrangements introduced: 0 746s Created read sampler 746s Sampling 202 reads 746s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 746s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 746s *** Run 71 of 100 746s /usr/bin/bowtie2 --trim3 6 --cp-ival 3 --local --mp 4.57877145809847,3.41163351851928 -N 1 -L13 --nofw --score-min L,2.36541138918138,6.40447093750352 -R 3 --cp-min 2 --norc -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s Parsed 94 reference bases 746s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '6' because it was < 2 characters long 746s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '7' because it was < 2 characters long 746s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '20' because it was < 2 characters long 746s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 746s Warning: skipping read '32' because it was < 2 characters long 746s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '40' because it was < 2 characters long 746s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '50' because it was < 2 characters long 746s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '58' because it was < 2 characters long 746s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '61' because it was < 2 characters long 746s Read 50 alignments... 746s Read 100 alignments... 746s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '95' because it was < 2 characters long 746s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '96' because it was < 2 characters long 746s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '105' because it was < 2 characters long 746s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '108' because it was < 2 characters long 746s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '109' because it was < 2 characters long 746s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '117' because it was < 2 characters long 746s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '121' because it was < 2 characters long 746s Warning: skipping mate #2 of read '128' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '128' because it was < 2 characters long 746s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '129' because it was < 2 characters long 746s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '137' because it was < 2 characters long 746s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '142' because it was < 2 characters long 746s Read 150 alignments... 746s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (1) 746s Read 200 alignments... 746s Warning: skipping mate #1 of read '145' because it was < 2 characters long 746s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '151' because it was < 2 characters long 746s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '156' because it was < 2 characters long 746s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '158' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '158' because it was < 2 characters long 746s Warning: skipping mate #2 of read '158' because it was < 2 characters long 746s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '164' because it was < 2 characters long 746s Warning: skipping mate #1 of read '172' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '172' because it was < 2 characters long 746s Warning: skipping mate #1 of read '176' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '176' because it was < 2 characters long 746s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '180' because it was < 2 characters long 746s Warning: skipping mate #1 of read '186' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '186' because it was < 2 characters long 746s Warning: skipping mate #1 of read '201' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '201' because it was < 2 characters long 746s Read 250 alignments... 746s Read 300 alignments... 746s 202 reads; of these: 746s 180 (89.11%) were paired; of these: 746s 180 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 180 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 180 pairs aligned 0 times concordantly or discordantly; of these: 746s 360 mates make up the pairs; of these: 746s 360 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 22 (10.89%) were unpaired; of these: 746s 22 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s Read 350 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s 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--trim3 6 --cp-ival 3 --local --mp 4.57877145809847,3.41163351851928 -N 1 -L13 --nofw --score-min L,2.36541138918138,6.40447093750352 -R 3 --cp-min 2 --norc -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s 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Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 0 alignments, 0 edits 746s --------------- 746s PASSED 746s ALSO checking that bowtie2 and bowtie2-align match up 746s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '6' because it was < 2 characters long 746s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '7' because it was < 2 characters long 746s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '20' because it was < 2 characters long 746s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 746s Warning: skipping read '32' because it was < 2 characters long 746s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '40' because it was < 2 characters long 746s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '50' because it was < 2 characters long 746s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '58' because it was < 2 characters long 746s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '61' because it was < 2 characters long 746s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '95' because it was < 2 characters long 746s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '96' because it was < 2 characters long 746s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '105' because it was < 2 characters long 746s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '108' because it was < 2 characters long 746s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '109' because it was < 2 characters long 746s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '117' because it was < 2 characters long 746s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '121' because it was < 2 characters long 746s Warning: skipping mate #2 of read '128' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '128' because it was < 2 characters long 746s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '129' because it was < 2 characters long 746s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '137' because it was < 2 characters long 746s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '142' because it was < 2 characters long 746s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '145' because it was < 2 characters long 746s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '151' because it was < 2 characters long 746s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '156' because it was < 2 characters long 746s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '158' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '158' because it was < 2 characters long 746s Warning: skipping mate #2 of read '158' because it was < 2 characters long 746s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '164' because it was < 2 characters long 746s Warning: skipping mate #1 of read '172' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '172' because it was < 2 characters long 746s Warning: skipping mate #1 of read '176' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '176' because it was < 2 characters long 746s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '180' because it was < 2 characters long 746s Warning: skipping mate #1 of read '186' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '186' because it was < 2 characters long 746s Warning: skipping mate #1 of read '201' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '201' because it was < 2 characters long 746s 202 reads; of these: 746s 180 (89.11%) were paired; of these: 746s 180 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 180 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 180 pairs aligned 0 times concordantly or discordantly; of these: 746s 360 mates make up the pairs; of these: 746s 360 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 22 (10.89%) were unpaired; of these: 746s 22 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 746s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 746s /usr/bin/bowtie2 --trim3 6 --cp-ival 3 --local --mp 4.57877145809847,3.41163351851928 -N 1 -L13 --nofw --score-min L,2.36541138918138,6.40447093750352 -R 3 --cp-min 2 --norc -f -p 4 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 746s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '6' because it was < 2 characters long 746s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '7' because it was < 2 characters long 746s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '20' because it was < 2 characters long 746s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 746s Warning: skipping read '32' because it was < 2 characters long 746s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '40' because it was < 2 characters long 746s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '50' because it was < 2 characters long 746s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '58' because it was < 2 characters long 746s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '61' because it was < 2 characters long 746s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '95' because it was < 2 characters long 746s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '96' because it was < 2 characters long 746s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '105' because it was < 2 characters long 746s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '108' because it was < 2 characters long 746s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '109' because it was < 2 characters long 746s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '117' because it was < 2 characters long 746s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '121' because it was < 2 characters long 746s Warning: skipping mate #2 of read '128' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '128' because it was < 2 characters long 746s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '129' because it was < 2 characters long 746s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '137' because it was < 2 characters long 746s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '142' because it was < 2 characters long 746s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '145' because it was < 2 characters long 746s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '151' because it was < 2 characters long 746s Warning: skipping mate #1 of read '156' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '156' because it was < 2 characters long 746s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #2 of read '158' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '158' because it was < 2 characters long 746s Warning: skipping mate #2 of read '158' because it was < 2 characters long 746s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '164' because it was < 2 characters long 746s Warning: skipping mate #1 of read '172' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '172' because it was < 2 characters long 746s Warning: skipping mate #1 of read '176' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '176' because it was < 2 characters long 746s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '180' because it was < 2 characters long 746s Warning: skipping mate #1 of read '186' because length (0) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '186' because it was < 2 characters long 746s Warning: skipping mate #1 of read '201' because length (1) <= # seed mismatches (1) 746s Warning: skipping mate #1 of read '201' because it was < 2 characters long 746s 202 reads; of these: 746s 180 (89.11%) were paired; of these: 746s 180 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 180 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 180 pairs aligned 0 times concordantly or discordantly; of these: 746s 360 mates make up the pairs; of these: 746s 360 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 22 (10.89%) were unpaired; of these: 746s 22 (100.00%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 0 (0.00%) aligned >1 times 746s 0.00% overall alignment rate 746s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 746s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 746s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.1 746s Introducing 0 SNPs, 1/2 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.2 746s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 2 746s Reference gaps introduced: 1 746s Read gaps introduced: 2 746s Rearrangements introduced: 0 746s Created read sampler 746s Sampling 49 reads 746s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 746s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s Parsed 94 reference bases 746s *** Run 72 of 100 746s /usr/bin/bowtie2 --rdg 44.4249388957954 --rfg 33.5301652741917 --score-min L,4.66844292675036,6.8003644589479 --mm --trim5 9 --cp-ival 2 --cp-min 2 --ma 9.11916470254259 --trim3 7 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 746s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 746s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '9' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 746s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '10' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 746s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '11' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 746s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '12' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 746s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '19' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 746s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 746s Warning: skipping read '21' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 746s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '22' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 746s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '24' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 746s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 746s Warning: skipping read '25' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 746s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '27' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 746s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '29' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 746s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '36' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 746s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '37' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 746s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '44' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 746s 49 reads; of these: 746s 37 (75.51%) were paired; of these: 746s 37 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 37 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 37 pairs aligned 0 times concordantly or discordantly; of these: 746s 74 mates make up the pairs; of these: 746s 72 (97.30%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 2 (2.70%) aligned >1 times 746s 12 (24.49%) were unpaired; of these: 746s 11 (91.67%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 1 (8.33%) aligned >1 times 746s 3.49% overall alignment rate 746s Read 50 alignments... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GGCGTCAACACC 746s GGCGTCAACACC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s AA 746s AA 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s GGCGTCAAC 746s GGCGTCAAC 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s Processing line... 746s --- Summary --- 746s Read 1 reference strings 746s Checked 3 alignments, 0 edits 746s --------------- 746s PASSED 746s ALSO checking that bowtie2 and bowtie2-align match up 746s /usr/bin/bowtie2 --rdg 44.4249388957954 --rfg 33.5301652741917 --score-min L,4.66844292675036,6.8003644589479 --mm --trim5 9 --cp-ival 2 --cp-min 2 --ma 9.11916470254259 --trim3 7 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 746s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 746s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '9' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 746s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '10' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 746s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '11' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 746s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '12' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 746s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '19' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 746s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 746s Warning: skipping read '21' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 746s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '22' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 746s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '24' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 746s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 746s Warning: skipping read '25' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 746s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '27' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 746s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '29' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 746s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '36' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 746s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '37' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 746s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 746s Warning: skipping mate #1 of read '44' because it was < 2 characters long 746s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 746s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 746s 49 reads; of these: 746s 37 (75.51%) were paired; of these: 746s 37 (100.00%) aligned concordantly 0 times 746s 0 (0.00%) aligned concordantly exactly 1 time 746s 0 (0.00%) aligned concordantly >1 times 746s ---- 746s 37 pairs aligned concordantly 0 times; of these: 746s 0 (0.00%) aligned discordantly 1 time 746s ---- 746s 37 pairs aligned 0 times concordantly or discordantly; of these: 746s 74 mates make up the pairs; of these: 746s 72 (97.30%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 2 (2.70%) aligned >1 times 746s 12 (24.49%) were unpaired; of these: 746s 11 (91.67%) aligned 0 times 746s 0 (0.00%) aligned exactly 1 time 746s 1 (8.33%) aligned >1 times 746s 3.49% overall alignment rate 746s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 746s Flattened IUPAC characters 746s Mutating sequence Sim.pm.1 746s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutating sequence Sim.pm.2 746s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 746s Finished SNPs 746s Finished ref gaps 746s Finished read gaps 746s Mutated reference genome to subject genome 746s SNPs introduced: 6 746s Reference gaps introduced: 0 746s Read gaps introduced: 0 746s Rearrangements introduced: 1 746s Created read sampler 746s Sampling 105 reads 746s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 746s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 746s parsing sequence Sim.pm.1... 746s parsing sequence Sim.pm.2... 746s Parsed 94 reference bases 746s *** Run 73 of 100 746s /usr/bin/bowtie2 -N 0 -L15 --cp-ival 1 --local -D 42 --trim3 4 --rdg 2.79765550503541 --score-min L,2.0429220649639,5.00360272606194 --mm --cp-min 2 --np 2 --trim5 6 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 747s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 747s 105 reads; of these: 747s 105 (100.00%) were unpaired; of these: 747s 105 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s Read 50 alignments... 747s Read 100 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s /usr/bin/bowtie2 -N 0 -L15 --cp-ival 1 --local -D 42 --trim3 4 --rdg 2.79765550503541 --score-min L,2.0429220649639,5.00360272606194 --mm --cp-min 2 --np 2 --trim5 6 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 0 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2-align match up 747s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 747s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 747s 105 reads; of these: 747s 105 (100.00%) were unpaired; of these: 747s 105 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.1 747s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.2 747s Introducing 7 SNPs, 1/1 ref/read gaps, and 1 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 7 747s Reference gaps introduced: 1 747s Read gaps introduced: 1 747s Rearrangements introduced: 1 747s Created read sampler 747s Sampling 92 reads 747s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 747s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 94 reference bases 747s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 747s *** Run 74 of 100 747s /usr/bin/bowtie2 --cp-ival 2 --local --cp-min 5 --trim3 6 --rdg 19.7576573311355 --score-min L,9.26404382309119,1.24374674294073 --np 1 -i C,4.66733503934158 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 747s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '6' because it was < 2 characters long 747s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '8' because it was < 2 characters long 747s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '9' because it was < 2 characters long 747s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '17' because it was < 2 characters long 747s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '18' because it was < 2 characters long 747s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '22' because it was < 2 characters long 747s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '24' because it was < 2 characters long 747s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '29' because it was < 2 characters long 747s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '31' because it was < 2 characters long 747s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '38' because it was < 2 characters long 747s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '45' because it was < 2 characters long 747s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '49' because it was < 2 characters long 747s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '51' because it was < 2 characters long 747s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '52' because it was < 2 characters long 747s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '55' because it was < 2 characters long 747s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '58' because it was < 2 characters long 747s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '59' because it was < 2 characters long 747s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '67' because it was < 2 characters long 747s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '70' because it was < 2 characters long 747s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '71' because it was < 2 characters long 747s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '75' because it was < 2 characters long 747s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '79' because it was < 2 characters long 747s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '82' because it was < 2 characters long 747s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '87' because it was < 2 characters long 747s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '92' because it was < 2 characters long 747s 92 reads; of these: 747s 92 (100.00%) were unpaired; of these: 747s 90 (97.83%) aligned 0 times 747s 2 (2.17%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 2.17% overall alignment rate 747s Read 50 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CATCATGAACATGGATTCAATCATA 747s CANCATGAACATGGATTCAATCATA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGAACATGGATTCAATCATAACAC 747s TGAACATGGATTCAATCATAACAC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 2 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2-align match up 747s /usr/bin/bowtie2 --cp-ival 2 --local --cp-min 5 --trim3 6 --rdg 19.7576573311355 --score-min L,9.26404382309119,1.24374674294073 --np 1 -i C,4.66733503934158 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 747s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '6' because it was < 2 characters long 747s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '8' because it was < 2 characters long 747s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '9' because it was < 2 characters long 747s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '17' because it was < 2 characters long 747s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '18' because it was < 2 characters long 747s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '22' because it was < 2 characters long 747s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '24' because it was < 2 characters long 747s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '29' because it was < 2 characters long 747s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '31' because it was < 2 characters long 747s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '38' because it was < 2 characters long 747s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '45' because it was < 2 characters long 747s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '49' because it was < 2 characters long 747s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '51' because it was < 2 characters long 747s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '52' because it was < 2 characters long 747s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '55' because it was < 2 characters long 747s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '58' because it was < 2 characters long 747s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '59' because it was < 2 characters long 747s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '67' because it was < 2 characters long 747s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '70' because it was < 2 characters long 747s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '71' because it was < 2 characters long 747s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '75' because it was < 2 characters long 747s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '79' because it was < 2 characters long 747s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '82' because it was < 2 characters long 747s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '87' because it was < 2 characters long 747s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '92' because it was < 2 characters long 747s 92 reads; of these: 747s 92 (100.00%) were unpaired; of these: 747s 90 (97.83%) aligned 0 times 747s 2 (2.17%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 2.17% overall alignment rate 747s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.1 747s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.2 747s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 9 747s Reference gaps introduced: 0 747s Read gaps introduced: 0 747s Rearrangements introduced: 1 747s Created read sampler 747s Sampling 167 reads 747s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 747s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 94 reference bases 747s *** Run 75 of 100 747s /usr/bin/bowtie2 --np 5 --score-min L,3.74464550954051,7.83492040353279 --rdg 17.6684432741337,3.28286889756278 --trim5 2 --mm --cp-min 2 --cp-ival 3 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Read 50 alignments... 747s Read 100 alignments... 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 747s Read 150 alignments... 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 747s Read 200 alignments... 747s 167 reads; of these: 747s 161 (96.41%) were paired; of these: 747s 160 (99.38%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 1 (0.62%) aligned concordantly >1 times 747s ---- 747s 160 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 160 pairs aligned 0 times concordantly or discordantly; of these: 747s 320 mates make up the pairs; of these: 747s 294 (91.88%) aligned 0 times 747s 2 (0.62%) aligned exactly 1 time 747s 24 (7.50%) aligned >1 times 747s 6 (3.59%) were unpaired; of these: 747s 6 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 8.54% overall alignment rate 747s Read 250 alignments... 747s Read 300 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GAA 747s GAA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CACCT 747s CACCT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TTGGCG 747s TTGGCG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s ACACC 747s ACACC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CCTG 747s CCTG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGGCGTCAACACCT 747s TGGCGTCAACACCT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGGCGTCAACA 747s TGGCGTCAACA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGGCGTCAA 747s TGGCGTCAA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGGCGT 747s TGGCGT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GCGTCAACACCTG 747s GCGTCAACACCTG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CCCGA 747s CCCGA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CCGAA 747s CCGAA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CACC 747s CACC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s ACACCT 747s ACACCT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s AC 747s AC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CGTCAACACCT 747s CGTCAACACCT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TC 747s TC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GCT 747s GCT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GCG 747s GCG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CA 747s CA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GCGTCAA 747s GCGTCAA 747s Processing line... 747s AC 747s AC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s ACCTG 747s ACCTG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TGGCGTC 747s TGGCGTC 747s Processing line... 747s Processing line... 747s CGT 747s CGT 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s GAAA 747s GAAA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CCCGAA 747s CCCGAA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s CTA 747s CTA 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 28 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2-align match up 747s /usr/bin/bowtie2 --np 5 --score-min L,3.74464550954051,7.83492040353279 --rdg 17.6684432741337,3.28286889756278 --trim5 2 --mm --cp-min 2 --cp-ival 3 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 747s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read 'R_1_1_1_125_125_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 747s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_151_151_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_155_155_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_160_160_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_164_164_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_166_166_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 747s 167 reads; of these: 747s 161 (96.41%) were paired; of these: 747s 160 (99.38%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 1 (0.62%) aligned concordantly >1 times 747s ---- 747s 160 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 160 pairs aligned 0 times concordantly or discordantly; of these: 747s 320 mates make up the pairs; of these: 747s 294 (91.88%) aligned 0 times 747s 2 (0.62%) aligned exactly 1 time 747s 24 (7.50%) aligned >1 times 747s 6 (3.59%) were unpaired; of these: 747s 6 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 8.54% overall alignment rate 747s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.1 747s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.2 747s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 3 747s Reference gaps introduced: 0 747s Read gaps introduced: 0 747s Rearrangements introduced: 2 747s Created read sampler 747s Sampling 52 reads 747s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 747s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 94 reference bases 747s *** Run 76 of 100 747s /usr/bin/bowtie2 --score-min L,9.55785579300381,9.73661574377322 --norc --rfg 2.90801680794984,4.04365203516112 --trim5 1 --cp-min 6 --cp-ival 2 -D 30 --local --trim3 9 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 747s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '1' because it was < 2 characters long 747s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '3' because it was < 2 characters long 747s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '7' because it was < 2 characters long 747s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '12' because it was < 2 characters long 747s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '15' because it was < 2 characters long 747s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '16' because it was < 2 characters long 747s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '26' because it was < 2 characters long 747s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '31' because it was < 2 characters long 747s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '32' because it was < 2 characters long 747s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '34' because it was < 2 characters long 747s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '36' because it was < 2 characters long 747s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '39' because it was < 2 characters long 747s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '40' because it was < 2 characters long 747s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '46' because it was < 2 characters long 747s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '47' because it was < 2 characters long 747s 52 reads; of these: 747s 52 (100.00%) were unpaired; of these: 747s 52 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s Read 50 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s /usr/bin/bowtie2 --score-min L,9.55785579300381,9.73661574377322 --norc --rfg 2.90801680794984,4.04365203516112 --trim5 1 --cp-min 6 --cp-ival 2 -D 30 --local --trim3 9 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 0 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2-align match up 747s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '1' because it was < 2 characters long 747s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '3' because it was < 2 characters long 747s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '7' because it was < 2 characters long 747s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '12' because it was < 2 characters long 747s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '15' because it was < 2 characters long 747s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '16' because it was < 2 characters long 747s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '26' because it was < 2 characters long 747s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '31' because it was < 2 characters long 747s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '32' because it was < 2 characters long 747s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '34' because it was < 2 characters long 747s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 747s Warning: skipping read '36' because it was < 2 characters long 747s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '39' because it was < 2 characters long 747s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '40' because it was < 2 characters long 747s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '46' because it was < 2 characters long 747s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '47' because it was < 2 characters long 747s 52 reads; of these: 747s 52 (100.00%) were unpaired; of these: 747s 52 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.2 747s Introducing 11 SNPs, 0/1 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.1 747s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 13 747s Reference gaps introduced: 1 747s Read gaps introduced: 1 747s Rearrangements introduced: 0 747s Created read sampler 747s Sampling 66 reads 747s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 747s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 94 reference bases 747s *** Run 77 of 100 747s /usr/bin/bowtie2 --mp 9.95398848368275,5.87203028198452 -N 1 -L24 --cp-ival 2 --n-ceil 0.498134059524813,0.242333666467276 --local --score-min L,6.30032537576168,7.79424020532073 --rfg 14.9519945485143,18.4104471876696 --gbar 1 --cp-min 2 --trim5 4 --np 2 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 747s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '8' because it was < 2 characters long 747s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '27' because it was < 2 characters long 747s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '36' because it was < 2 characters long 747s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '37' because it was < 2 characters long 747s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '38' because it was < 2 characters long 747s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '54' because it was < 2 characters long 747s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '60' because it was < 2 characters long 747s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '66' because it was < 2 characters long 747s Read 50 alignments... 747s 66 reads; of these: 747s 61 (92.42%) were paired; of these: 747s 61 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 61 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 61 pairs aligned 0 times concordantly or discordantly; of these: 747s 122 mates make up the pairs; of these: 747s 122 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 5 (7.58%) were unpaired; of these: 747s 5 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s Read 100 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 0 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 747s /usr/bin/bowtie2 --mp 9.95398848368275,5.87203028198452 -N 1 -L24 --cp-ival 2 --n-ceil 0.498134059524813,0.242333666467276 --local --score-min L,6.30032537576168,7.79424020532073 --rfg 14.9519945485143,18.4104471876696 --gbar 1 --cp-min 2 --trim5 4 --np 2 -f -p 4 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 747s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '8' because it was < 2 characters long 747s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '27' because it was < 2 characters long 747s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '36' because it was < 2 characters long 747s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '37' because it was < 2 characters long 747s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '38' because it was < 2 characters long 747s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '54' because it was < 2 characters long 747s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '60' because it was < 2 characters long 747s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '66' because it was < 2 characters long 747s 66 reads; of these: 747s 61 (92.42%) were paired; of these: 747s 61 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 61 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 61 pairs aligned 0 times concordantly or discordantly; of these: 747s 122 mates make up the pairs; of these: 747s 122 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 5 (7.58%) were unpaired; of these: 747s 5 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 747s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 747s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 747s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 747s /usr/bin/bowtie2 --mp 9.95398848368275,5.87203028198452 -N 1 -L24 --cp-ival 2 --n-ceil 0.498134059524813,0.242333666467276 --local --score-min L,6.30032537576168,7.79424020532073 --rfg 14.9519945485143,18.4104471876696 --gbar 1 --cp-min 2 --trim5 4 --np 2 -f -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 747s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '8' because it was < 2 characters long 747s Warning: skipping mate #2 of read '27' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '27' because it was < 2 characters long 747s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '36' because it was < 2 characters long 747s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '37' because it was < 2 characters long 747s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '38' because it was < 2 characters long 747s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '54' because it was < 2 characters long 747s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '60' because it was < 2 characters long 747s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '66' because it was < 2 characters long 747s 66 reads; of these: 747s 61 (92.42%) were paired; of these: 747s 61 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 61 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 61 pairs aligned 0 times concordantly or discordantly; of these: 747s 122 mates make up the pairs; of these: 747s 122 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 5 (7.58%) were unpaired; of these: 747s 5 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.2 747s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.1 747s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 6 747s Reference gaps introduced: 0 747s Read gaps introduced: 0 747s Rearrangements introduced: 2 747s Created read sampler 747s Sampling 43 reads 747s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 747s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 94 reference bases 747s *** Run 78 of 100 747s /usr/bin/bowtie2 --score-min L,6.74774068107734,7.06797900319948 --rfg 5.5437673349959,3.51986867803561 --rdg 24.5494930863878 --mm --mp 3.9960286401503,3.0434191882101 --cp-ival 1 --local --trim3 7 --norc --np 5 --trim5 9 --cp-min 3 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 747s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '1' because it was < 2 characters long 747s Warning: skipping mate #2 of read '1' because it was < 2 characters long 747s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '5' because it was < 2 characters long 747s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '10' because it was < 2 characters long 747s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '15' because it was < 2 characters long 747s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '17' because it was < 2 characters long 747s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '19' because it was < 2 characters long 747s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '23' because it was < 2 characters long 747s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '24' because it was < 2 characters long 747s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '26' because it was < 2 characters long 747s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '28' because it was < 2 characters long 747s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '35' because it was < 2 characters long 747s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '40' because it was < 2 characters long 747s Warning: skipping mate #2 of read '40' because it was < 2 characters long 747s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '42' because it was < 2 characters long 747s 43 reads; of these: 747s 34 (79.07%) were paired; of these: 747s 34 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 34 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 34 pairs aligned 0 times concordantly or discordantly; of these: 747s 68 mates make up the pairs; of these: 747s 68 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 9 (20.93%) were unpaired; of these: 747s 9 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s Read 50 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 0 alignments, 0 edits 747s --------------- 747s PASSED 747s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 747s /usr/bin/bowtie2 --score-min L,6.74774068107734,7.06797900319948 --rfg 5.5437673349959,3.51986867803561 --rdg 24.5494930863878 --mm --mp 3.9960286401503,3.0434191882101 --cp-ival 1 --local --trim3 7 --norc --np 5 --trim5 9 --cp-min 3 -q -p 2 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 747s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '1' because it was < 2 characters long 747s Warning: skipping mate #2 of read '1' because it was < 2 characters long 747s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '5' because it was < 2 characters long 747s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '10' because it was < 2 characters long 747s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '15' because it was < 2 characters long 747s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '17' because it was < 2 characters long 747s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '19' because it was < 2 characters long 747s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '23' because it was < 2 characters long 747s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 747s Warning: skipping read '24' because it was < 2 characters long 747s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '26' because it was < 2 characters long 747s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '28' because it was < 2 characters long 747s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '35' because it was < 2 characters long 747s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '40' because it was < 2 characters long 747s Warning: skipping mate #2 of read '40' because it was < 2 characters long 747s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '42' because it was < 2 characters long 747s 43 reads; of these: 747s 34 (79.07%) were paired; of these: 747s 34 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 34 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 34 pairs aligned 0 times concordantly or discordantly; of these: 747s 68 mates make up the pairs; of these: 747s 68 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 9 (20.93%) were unpaired; of these: 747s 9 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 747s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 747s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.1 747s Introducing 2 SNPs, 1/1 ref/read gaps, and 1 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.2 747s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 6 747s Reference gaps introduced: 1 747s Read gaps introduced: 2 747s Rearrangements introduced: 1 747s Created read sampler 747s Sampling 107 reads 747s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 747s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 94 reference bases 747s *** Run 79 of 100 747s /usr/bin/bowtie2 --rdg 7.93597890183246 --norc --score-min L,9.90282537403524,1.97643522219592 --trim3 3 --cp-ival 2 --local --cp-min 3 -N 1 -L19 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 747s Warning: skipping mate #1 of read '0' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '0' because it was < 2 characters long 747s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '17' because it was < 2 characters long 747s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '22' because it was < 2 characters long 747s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '47' because it was < 2 characters long 747s Warning: skipping mate #1 of read '57' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '57' because it was < 2 characters long 747s Read 50 alignments... 747s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '81' because it was < 2 characters long 747s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '82' because it was < 2 characters long 747s Warning: skipping mate #2 of read '84' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #2 of read '84' because it was < 2 characters long 747s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '93' because it was < 2 characters long 747s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '95' because it was < 2 characters long 747s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '100' because it was < 2 characters long 747s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (1) 747s Warning: skipping mate #1 of read '106' because it was < 2 characters long 747s Read 100 alignments... 747s 107 reads; of these: 747s 99 (92.52%) were paired; of these: 747s 99 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 99 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 99 pairs aligned 0 times concordantly or discordantly; of these: 747s 198 mates make up the pairs; of these: 747s 198 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 8 (7.48%) were unpaired; of these: 747s 8 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 0.00% overall alignment rate 747s Read 150 alignments... 747s Read 200 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 0 alignments, 0 edits 747s --------------- 747s PASSED 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.2 747s Introducing 11 SNPs, 0/0 ref/read gaps, and 2 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutating sequence Sim.pm.1 747s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 12 747s Reference gaps introduced: 0 747s Read gaps introduced: 0 747s Rearrangements introduced: 2 747s Created read sampler 747s Sampling 35 reads 747s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 747s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 94 reference bases 747s *** Run 80 of 100 747s /usr/bin/bowtie2 --mm --trim5 9 -k 2 --norc --rdg 26.8114476008215,12.3555704332998 --score-min L,6.98724148278848,2.89070965708714 --mp 4.80367416903018,2.85054418737826 --cp-ival 3 --cp-min 4 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 747s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '2' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 747s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '25' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 747s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 747s Warning: skipping mate #1 of read '31' because it was < 2 characters long 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 747s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 747s 35 reads; of these: 747s 30 (85.71%) were paired; of these: 747s 30 (100.00%) aligned concordantly 0 times 747s 0 (0.00%) aligned concordantly exactly 1 time 747s 0 (0.00%) aligned concordantly >1 times 747s ---- 747s 30 pairs aligned concordantly 0 times; of these: 747s 0 (0.00%) aligned discordantly 1 time 747s ---- 747s 30 pairs aligned 0 times concordantly or discordantly; of these: 747s 60 mates make up the pairs; of these: 747s 57 (95.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 3 (5.00%) aligned >1 times 747s 5 (14.29%) were unpaired; of these: 747s 5 (100.00%) aligned 0 times 747s 0 (0.00%) aligned exactly 1 time 747s 0 (0.00%) aligned >1 times 747s 4.62% overall alignment rate 747s Read 50 alignments... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TTGGCGTCAAC 747s TTGGCGTCAAC 747s Processing line... 747s TTGGCGTCAAC 747s TTGGCGTCAAC 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TG 747s TG 747s Processing line... 747s TG 747s TG 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s TA 747s TA 747s Processing line... 747s TA 747s TA 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s Processing line... 747s --- Summary --- 747s Read 1 reference strings 747s Checked 6 alignments, 0 edits 747s --------------- 747s PASSED 747s Flattened IUPAC characters 747s Mutating sequence Sim.pm.2 747s Introducing 6 SNPs, 1/1 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s *** Run 81 of 100 747s /usr/bin/bowtie2 -i C,1.60698519861034 --trim5 9 -k 3 --ma 30.5042385737692 --cp-min 11 --mm --rdg 31.4196028433117 --rfg 3.793598270256 --score-min L,6.47593284233208,4.56606702791327 --gbar 4 --trim3 5 --mp 8.61174247553484,5.42511623964407 --cp-ival 1 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 747s Finished read gaps 747s Mutating sequence Sim.pm.1 747s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 747s Finished SNPs 747s Finished ref gaps 747s Finished read gaps 747s Mutated reference genome to subject genome 747s SNPs introduced: 10 747s Reference gaps introduced: 2 747s Read gaps introduced: 1 747s Rearrangements introduced: 0 747s Created read sampler 747s Sampling 81 reads 747s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 747s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 747s parsing sequence Sim.pm.1... 747s parsing sequence Sim.pm.2... 747s Parsed 94 reference bases 748s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 748s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 748s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '9' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 748s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '11' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 748s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '15' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 748s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '17' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 748s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '20' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 748s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '21' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 748s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '22' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 748s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '25' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 748s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '26' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 748s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '29' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 748s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '30' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 748s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '32' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 748s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '33' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 748s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '35' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 748s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '37' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 748s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '38' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 748s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '40' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 748s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '41' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 748s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '42' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 748s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '43' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 748s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '49' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 748s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '57' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 748s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '61' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 748s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '64' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 748s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '65' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 748s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '70' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 748s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '71' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 748s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '72' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 748s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '74' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 748s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '79' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 748s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '80' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 748s 81 reads; of these: 748s 81 (100.00%) were unpaired; of these: 748s 78 (96.30%) aligned 0 times 748s 3 (3.70%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 3.70% overall alignment rate 748s Read 50 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TGGATTCA 748s TGGATTCA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s ATGCTA 748s ATGCTA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CATGGATTCAATC 748s CATGGATTCAATC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 3 alignments, 0 edits 748s --------------- 748s PASSED 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.2 748s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.1 748s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 8 748s Reference gaps introduced: 0 748s Read gaps introduced: 0 748s Rearrangements introduced: 0 748s Created read sampler 748s Sampling 121 reads 748s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 748s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 94 reference bases 748s *** Run 82 of 100 748s /usr/bin/bowtie2 -R 2 --n-ceil 1.17936638591166,0.956515425957652 --cp-ival 1 --cp-min 3 --mp 8.62991500810849,8.2370864512177 -i L,0.321329269703938 --mm --rdg 4.46120970426259,19.2243225798325 --score-min L,2.95972140579313,1.13922483373159 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 748s 121 reads; of these: 748s 121 (100.00%) were unpaired; of these: 748s 93 (76.86%) aligned 0 times 748s 14 (11.57%) aligned exactly 1 time 748s 14 (11.57%) aligned >1 times 748s 23.14% overall alignment rate 748s Read 50 alignments... 748s Read 100 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s ACATGGATTCAATCATAACACATTT 748s ACATGGATTCAATCATAACACATTT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TT 748s TT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TC 748s TC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CCCGAAA 748s CCCGAAA 748s Processing line... 748s Processing line... 748s Processing line... 748s ACATG 748s ACATG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s AA 748s AA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TCA 748s TCA 748s Processing line... 748s CCCGA 748s CCCGA 748s Processing line... 748s ATGGATTCA 748s ATGGATTCA 748s Processing line... 748s Processing line... 748s AAC 748s AAC 748s Processing line... 748s Processing line... 748s Processing line... 748s TCATAACACA 748s TCATAACACA 748s Processing line... 748s Processing line... 748s GGA 748s GGA 748s Processing line... 748s Processing line... 748s TGGCGTCAACA 748s TGGCGTCAACA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TAAC 748s TAAC 748s Processing line... 748s Processing line... 748s Processing line... 748s TGGATTCAATCA 748s TGGATTCAATCA 748s Processing line... 748s Processing line... 748s Processing line... 748s GAACATGG 748s GAACATGG 748s Processing line... 748s Processing line... 748s CAATCATA 748s CAATCATA 748s Processing line... 748s Processing line... 748s GG 748s GG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s AAA 748s AAA 748s Processing line... 748s Processing line... 748s CAATCAT 748s CAATCAT 748s Processing line... 748s Processing line... 748s TGCT 748s TGCT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s AT 748s AT 748s Processing line... 748s AACATGGATT 748s AACATGGATT 748s Processing line... 748s AAA 748s AAA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CTG 748s CTG 748s Processing line... 748s ATGCT 748s ATGCT 748s Processing line... 748s Processing line... 748s Processing line... 748s TCATAACACAT 748s TCATAACACAT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CGTCAAC 748s CGTCAAC 748s --- Summary --- 748s Read 1 reference strings 748s Checked 28 alignments, 0 edits 748s --------------- 748s PASSED 748s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 748s /usr/bin/bowtie2 -R 2 --n-ceil 1.17936638591166,0.956515425957652 --cp-ival 1 --cp-min 3 --mp 8.62991500810849,8.2370864512177 -i L,0.321329269703938 --mm --rdg 4.46120970426259,19.2243225798325 --score-min L,2.95972140579313,1.13922483373159 --qseq -p 3 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 748s 121 reads; of these: 748s 121 (100.00%) were unpaired; of these: 748s 93 (76.86%) aligned 0 times 748s 14 (11.57%) aligned exactly 1 time 748s 14 (11.57%) aligned >1 times 748s 23.14% overall alignment rate 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 748s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 748s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 748s /usr/bin/bowtie2 -R 2 --n-ceil 1.17936638591166,0.956515425957652 --cp-ival 1 --cp-min 3 --mp 8.62991500810849,8.2370864512177 -i L,0.321329269703938 --mm --rdg 4.46120970426259,19.2243225798325 --score-min L,2.95972140579313,1.13922483373159 --qseq -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 748s 121 reads; of these: 748s 121 (100.00%) were unpaired; of these: 748s 93 (76.86%) aligned 0 times 748s 14 (11.57%) aligned exactly 1 time 748s 14 (11.57%) aligned >1 times 748s 23.14% overall alignment rate 748s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.2 748s Introducing 10 SNPs, 0/1 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.1 748s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 13 748s Reference gaps introduced: 1 748s Read gaps introduced: 1 748s Rearrangements introduced: 1 748s Created read sampler 748s Sampling 108 reads 748s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 748s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 94 reference bases 748s *** Run 83 of 100 748s /usr/bin/bowtie2 --mp 7.4850790380648,2.05166366947415 --cp-ival 1 --local --score-min L,4.90877377998353,1.17338262020495 --rfg 40.1174346669493 --rdg 31.7686677790884,12.6860292792844 --mm --cp-min 5 -R 4 --np 3 --trim5 5 --qseq -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.qseq -2 /tmp/Sim.pm.WCUbbuUs_2.qseq 748s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 748s Read 50 alignments... 748s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 748s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 748s Warning: skipping mate #2 of read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 748s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 748s Warning: skipping mate #2 of read 'R_1_1_1_91_91_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 748s 108 reads; of these: 748s 99 (91.67%) were paired; of these: 748s 99 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 99 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 99 pairs aligned 0 times concordantly or discordantly; of these: 748s 198 mates make up the pairs; of these: 748s 194 (97.98%) aligned 0 times 748s 3 (1.52%) aligned exactly 1 time 748s 1 (0.51%) aligned >1 times 748s 9 (8.33%) were unpaired; of these: 748s 8 (88.89%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 1 (11.11%) aligned >1 times 748s 2.42% overall alignment rate 748s Read 100 alignments... 748s Read 150 alignments... 748s Read 200 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s AACAC 748s AACAC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s ATAACACA 748s ATAACACA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CAACACCTG 748s CAACACCTG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GATTCAATCATAACACAT 748s GATTCAATCATAACACAT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s ATTCAATCATAACA 748s ATTCAATCATAACA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 5 alignments, 0 edits 748s --------------- 748s PASSED 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 14 SNPs, 0/0 ref/read gaps, and 1 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 22 748s Reference gaps introduced: 0 748s Read gaps introduced: 0 748s Rearrangements introduced: 2 748s Created read sampler 748s Sampling 199 reads 748s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 748s *** Run 84 of 100 748s /usr/bin/bowtie2 --rfg 5.63425451932086 --score-min L,8.29362767513765,8.1841563399198 --mm -a -D 42 --cp-ival 3 --cp-min 7 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 748s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 94 reference bases 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 748s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '13' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 748s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '19' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 748s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '23' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 748s Read 50 alignments... 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 748s Read 100 alignments... 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 748s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '99' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 748s Warning: skipping mate #2 of read '129' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '129' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 748s Warning: skipping mate #2 of read '138' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '138' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 748s Read 150 alignments... 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 748s Read 200 alignments... 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 748s Warning: skipping mate #2 of read '147' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '147' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 748s Warning: skipping mate #2 of read '162' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '162' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 748s Warning: skipping mate #2 of read '187' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '187' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 748s Warning: skipping mate #1 of read '199' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '199' because it was < 2 characters long 748s Read 250 alignments... 748s 199 reads; of these: 748s 199 (100.00%) were paired; of these: 748s 198 (99.50%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 1 (0.50%) aligned concordantly >1 times 748s ---- 748s 198 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 198 pairs aligned 0 times concordantly or discordantly; of these: 748s 396 mates make up the pairs; of these: 748s 374 (94.44%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 22 (5.56%) aligned >1 times 748s 6.03% overall alignment rate 748s Read 300 alignments... 748s Read 350 alignments... 748s Read 400 alignments... 748s Read 450 alignments... 748s Read 500 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s ACAT 748s ACAT 748s Processing line... 748s ACAT 748s ACAT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CT 748s CT 748s Processing line... 748s CT 748s CT 748s Processing line... 748s CT 748s CT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GTC 748s GTC 748s Processing line... 748s GTC 748s GTC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GTCAACA 748s GTCAACA 748s Processing line... 748s GTCAACA 748s GTCAACA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GCGTCAACACCTG 748s GCGTCAACACCTG 748s Processing line... 748s GCGTCAACACCTG 748s GCGTCAACACCTG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CCT 748s CCT 748s Processing line... 748s CCT 748s CCT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s AC 748s AC 748s Processing line... 748s GT 748s GT 748s Processing line... 748s AC 748s AC 748s Processing line... 748s AC 748s AC 748s Processing line... 748s AC 748s AC 748s Processing line... 748s AC 748s AC 748s Processing line... 748s AC 748s AC 748s Processing line... 748s GT 748s GT 748s Processing line... 748s AC 748s AC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s ACC 748s ACC 748s Processing line... 748s ACC 748s ACC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CGAA 748s CGAA 748s Processing line... 748s CGAA 748s CGAA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GGC 748s GGC 748s Processing line... 748s GGC 748s GGC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CT 748s CT 748s Processing line... 748s CT 748s CT 748s Processing line... 748s CT 748s CT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s GTCA 748s GTCA 748s Processing line... 748s GTCA 748s GTCA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing 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CA 748s CA 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s CA 748s CA 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CGTC 748s CGTC 748s Processing line... 748s CGTC 748s CGTC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing 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Processing line... 748s Processing line... 748s Processing line... 748s CCG 748s CCG 748s Processing line... 748s CCG 748s CCG 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TG 748s TG 748s Processing line... 748s CA 748s CA 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s CA 748s CA 748s Processing line... 748s TG 748s TG 748s Processing line... 748s TG 748s TG 748s Processing line... 748s CA 748s CA 748s Processing line... 748s CA 748s CA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CAA 748s CAA 748s Processing line... 748s GA 748s GA 748s Processing line... 748s CAA 748s CAA 748s Processing line... 748s GA 748s GA 748s Processing line... 748s CAA 748s CAA 748s Processing line... 748s GA 748s GA 748s Processing line... 748s TTG 748s TTG 748s Processing line... 748s TC 748s TC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 130 alignments, 0 edits 748s --------------- 748s PASSED 748s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 748s /usr/bin/bowtie2 --rfg 5.63425451932086 --score-min L,8.29362767513765,8.1841563399198 --mm -a -D 42 --cp-ival 3 --cp-min 7 -q -p 4 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 748s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '13' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 748s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '19' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 748s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '23' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 748s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '99' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 748s Warning: skipping mate #2 of read '129' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '129' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 748s Warning: skipping mate #2 of read '138' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '138' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 748s Warning: skipping mate #2 of read '162' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '162' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 748s Warning: skipping mate #2 of read '147' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '147' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 748s Warning: skipping mate #2 of read '187' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '187' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 748s Warning: skipping mate #1 of read '199' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '199' because it was < 2 characters long 748s 199 reads; of these: 748s 199 (100.00%) were paired; of these: 748s 198 (99.50%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 1 (0.50%) aligned concordantly >1 times 748s ---- 748s 198 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 198 pairs aligned 0 times concordantly or discordantly; of these: 748s 396 mates make up the pairs; of these: 748s 374 (94.44%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 22 (5.56%) aligned >1 times 748s 6.03% overall alignment rate 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 748s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.2 748s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.1 748s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 8 748s Reference gaps introduced: 1 748s Read gaps introduced: 1 748s Rearrangements introduced: 0 748s Created read sampler 748s Sampling 63 reads 748s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 748s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s Parsed 94 reference bases 748s *** Run 85 of 100 748s /usr/bin/bowtie2 --rdg 3.26335027785263,9.46748766942716 --score-min L,4.8033428491485,1.23893334265302 -i L,0.0626039632229772 --cp-ival 3 --local --cp-min 9 --trim3 9 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 748s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '5' because it was < 2 characters long 748s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '7' because it was < 2 characters long 748s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '9' because it was < 2 characters long 748s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '10' because it was < 2 characters long 748s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '15' because it was < 2 characters long 748s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '18' because it was < 2 characters long 748s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '20' because it was < 2 characters long 748s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '21' because it was < 2 characters long 748s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '22' because it was < 2 characters long 748s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '27' because it was < 2 characters long 748s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '28' because it was < 2 characters long 748s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '29' because it was < 2 characters long 748s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '33' because it was < 2 characters long 748s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '34' because it was < 2 characters long 748s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '42' because it was < 2 characters long 748s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '57' because it was < 2 characters long 748s 63 reads; of these: 748s 50 (79.37%) were paired; of these: 748s 50 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 50 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 50 pairs aligned 0 times concordantly or discordantly; of these: 748s 100 mates make up the pairs; of these: 748s 97 (97.00%) aligned 0 times 748s 1 (1.00%) aligned exactly 1 time 748s 2 (2.00%) aligned >1 times 748s 13 (20.63%) were unpaired; of these: 748s 13 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 2.65% overall alignment rate 748s Read 50 alignments... 748s Read 100 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CACAT 748s CACAT 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s /usr/bin/bowtie2 --rdg 3.26335027785263,9.46748766942716 --score-min L,4.8033428491485,1.23893334265302 -i L,0.0626039632229772 --cp-ival 3 --local --cp-min 9 --trim3 9 -q -p 3 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s TTGGCGTCAAC 748s TTGGCGTCAAC 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s CCGAA 748s CCGAA 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 3 alignments, 0 edits 748s --------------- 748s PASSED 748s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 748s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '5' because it was < 2 characters long 748s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '7' because it was < 2 characters long 748s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '9' because it was < 2 characters long 748s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '10' because it was < 2 characters long 748s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '15' because it was < 2 characters long 748s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '18' because it was < 2 characters long 748s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '20' because it was < 2 characters long 748s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '21' because it was < 2 characters long 748s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '22' because it was < 2 characters long 748s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '27' because it was < 2 characters long 748s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '28' because it was < 2 characters long 748s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '29' because it was < 2 characters long 748s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '33' because it was < 2 characters long 748s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '34' because it was < 2 characters long 748s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '42' because it was < 2 characters long 748s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '57' because it was < 2 characters long 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 748s 63 reads; of these: 748s 50 (79.37%) were paired; of these: 748s 50 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 50 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 50 pairs aligned 0 times concordantly or discordantly; of these: 748s 100 mates make up the pairs; of these: 748s 97 (97.00%) aligned 0 times 748s 1 (1.00%) aligned exactly 1 time 748s 2 (2.00%) aligned >1 times 748s 13 (20.63%) were unpaired; of these: 748s 13 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 2.65% overall alignment rate 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 748s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 748s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 748s /usr/bin/bowtie2 --rdg 3.26335027785263,9.46748766942716 --score-min L,4.8033428491485,1.23893334265302 -i L,0.0626039632229772 --cp-ival 3 --local --cp-min 9 --trim3 9 -q -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 748s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '5' because it was < 2 characters long 748s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '7' because it was < 2 characters long 748s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '9' because it was < 2 characters long 748s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '10' because it was < 2 characters long 748s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '15' because it was < 2 characters long 748s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '18' because it was < 2 characters long 748s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '20' because it was < 2 characters long 748s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '21' because it was < 2 characters long 748s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '22' because it was < 2 characters long 748s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '27' because it was < 2 characters long 748s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '28' because it was < 2 characters long 748s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '29' because it was < 2 characters long 748s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '33' because it was < 2 characters long 748s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '34' because it was < 2 characters long 748s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '42' because it was < 2 characters long 748s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 748s Warning: skipping read '57' because it was < 2 characters long 748s 63 reads; of these: 748s 50 (79.37%) were paired; of these: 748s 50 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 50 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 50 pairs aligned 0 times concordantly or discordantly; of these: 748s 100 mates make up the pairs; of these: 748s 97 (97.00%) aligned 0 times 748s 1 (1.00%) aligned exactly 1 time 748s 2 (2.00%) aligned >1 times 748s 13 (20.63%) were unpaired; of these: 748s 13 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 2.65% overall alignment rate 748s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.1 748s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.2 748s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 3 748s Reference gaps introduced: 0 748s Read gaps introduced: 0 748s Rearrangements introduced: 4 748s Created read sampler 748s Sampling 32 reads 748s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 748s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 748s parsing sequence Sim.pm.1... 748s *** Run 86 of 100 748s /usr/bin/bowtie2 --trim5 8 --norc --cp-min 4 --ma 6.02086895507475 --mm --gbar 1 --rfg 24.1810708918567 --rdg 29.2633287326353 --score-min L,3.13861537900861,1.86810356601551 --cp-ival 1 --n-ceil 0.315018023027355,0.0833569441853744 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 748s parsing sequence Sim.pm.2... 748s Parsed 94 reference bases 748s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 748s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 748s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 748s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 748s 32 reads; of these: 748s 32 (100.00%) were unpaired; of these: 748s 32 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 0 alignments, 0 edits 748s --------------- 748s PASSED 748s Flattened IUPAC characters 748s Mutating sequence Sim.pm.2 748s Introducing 12 SNPs, 0/0 ref/read gaps, and 2 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutating sequence Sim.pm.1 748s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 748s Finished SNPs 748s Finished ref gaps 748s Finished read gaps 748s Mutated reference genome to subject genome 748s SNPs introduced: 19 748s Reference gaps introduced: 0 748s Read gaps introduced: 0 748s Rearrangements introduced: 2 748s Created read sampler 748s Sampling 203 reads 748s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 748s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 748s parsing sequence Sim.pm.1... 748s parsing sequence Sim.pm.2... 748s *** Run 87 of 100 748s /usr/bin/bowtie2 --cp-min 5 --score-min L,7.98672625649336,5.68406291918147 --rfg 35.8697289898652,7.86470408481539 --mm -a --nofw --local --cp-ival 1 --n-ceil 1.31447528034002,0.259518847828313 --trim3 1 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 748s Parsed 94 reference bases 748s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '51' because it was < 2 characters long 748s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '54' because it was < 2 characters long 748s Read 50 alignments... 748s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '85' because it was < 2 characters long 748s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '87' because it was < 2 characters long 748s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '88' because it was < 2 characters long 748s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '95' because it was < 2 characters long 748s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '96' because it was < 2 characters long 748s Warning: skipping mate #2 of read '123' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '123' because it was < 2 characters long 748s Warning: skipping mate #1 of read '156' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '156' because it was < 2 characters long 748s Read 100 alignments... 748s Read 150 alignments... 748s Read 200 alignments... 748s Warning: skipping mate #1 of read '166' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '166' because it was < 2 characters long 748s Read 250 alignments... 748s Read 300 alignments... 748s Warning: skipping mate #1 of read '185' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '185' because it was < 2 characters long 748s Warning: skipping mate #2 of read '201' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '201' because it was < 2 characters long 748s 203 reads; of these: 748s 200 (98.52%) were paired; of these: 748s 200 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 200 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 200 pairs aligned 0 times concordantly or discordantly; of these: 748s 400 mates make up the pairs; of these: 748s 400 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 3 (1.48%) were unpaired; of these: 748s 3 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s Read 350 alignments... 748s Read 400 alignments... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s /usr/bin/bowtie2 --cp-min 5 --score-min L,7.98672625649336,5.68406291918147 --rfg 35.8697289898652,7.86470408481539 --mm -a --nofw --local --cp-ival 1 --n-ceil 1.31447528034002,0.259518847828313 --trim3 1 -q -p 2 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s 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line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s Processing line... 748s --- Summary --- 748s Read 1 reference strings 748s Checked 0 alignments, 0 edits 748s --------------- 748s PASSED 748s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 748s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '51' because it was < 2 characters long 748s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '54' because it was < 2 characters long 748s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '85' because it was < 2 characters long 748s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '87' because it was < 2 characters long 748s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '88' because it was < 2 characters long 748s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '95' because it was < 2 characters long 748s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '96' because it was < 2 characters long 748s Warning: skipping mate #2 of read '123' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '123' because it was < 2 characters long 748s Warning: skipping mate #1 of read '156' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '156' because it was < 2 characters long 748s Warning: skipping mate #1 of read '166' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '166' because it was < 2 characters long 748s Warning: skipping mate #1 of read '185' because length (0) <= # seed mismatches (0) 748s Warning: skipping mate #1 of read '185' because it was < 2 characters long 748s Warning: skipping mate #2 of read '201' because length (1) <= # seed mismatches (0) 748s Warning: skipping mate #2 of read '201' because it was < 2 characters long 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 748s 203 reads; of these: 748s 200 (98.52%) were paired; of these: 748s 200 (100.00%) aligned concordantly 0 times 748s 0 (0.00%) aligned concordantly exactly 1 time 748s 0 (0.00%) aligned concordantly >1 times 748s ---- 748s 200 pairs aligned concordantly 0 times; of these: 748s 0 (0.00%) aligned discordantly 1 time 748s ---- 748s 200 pairs aligned 0 times concordantly or discordantly; of these: 748s 400 mates make up the pairs; of these: 748s 400 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 3 (1.48%) were unpaired; of these: 748s 3 (100.00%) aligned 0 times 748s 0 (0.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 0.00% overall alignment rate 748s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 748s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 748s /usr/bin/bowtie2 --cp-min 5 --score-min L,7.98672625649336,5.68406291918147 --rfg 35.8697289898652,7.86470408481539 --mm -a --nofw --local --cp-ival 1 --n-ceil 1.31447528034002,0.259518847828313 --trim3 1 -q -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 748s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 749s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '51' because it was < 2 characters long 749s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '54' because it was < 2 characters long 749s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '85' because it was < 2 characters long 749s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '87' because it was < 2 characters long 749s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '88' because it was < 2 characters long 749s Warning: skipping mate #1 of read '95' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '95' because it was < 2 characters long 749s Warning: skipping mate #2 of read '96' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '96' because it was < 2 characters long 749s Warning: skipping mate #2 of read '123' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '123' because it was < 2 characters long 749s Warning: skipping mate #1 of read '156' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '156' because it was < 2 characters long 749s Warning: skipping mate #1 of read '166' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '166' because it was < 2 characters long 749s Warning: skipping mate #1 of read '185' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '185' because it was < 2 characters long 749s Warning: skipping mate #2 of read '201' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '201' because it was < 2 characters long 749s 203 reads; of these: 749s 200 (98.52%) were paired; of these: 749s 200 (100.00%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 0 (0.00%) aligned concordantly >1 times 749s ---- 749s 200 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 749s ---- 749s 200 pairs aligned 0 times concordantly or discordantly; of these: 749s 400 mates make up the pairs; of these: 749s 400 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 3 (1.48%) were unpaired; of these: 749s 3 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.2 749s Introducing 6 SNPs, 0/0 ref/read gaps, and 3 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.1 749s Introducing 2 SNPs, 2/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 8 749s Reference gaps introduced: 2 749s Read gaps introduced: 0 749s Rearrangements introduced: 3 749s Created read sampler 749s Sampling 107 reads 749s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 749s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 749s parsing sequence Sim.pm.1... 749s parsing sequence Sim.pm.2... 749s Parsed 94 reference bases 749s *** Run 88 of 100 749s /usr/bin/bowtie2 --score-min L,8.09189128820354,7.40802751420175 --trim3 9 --cp-ival 2 -D 29 --local -M 9 --norc --cp-min 10 -f -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fasta 749s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 749s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '7' because it was < 2 characters long 749s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '8' because it was < 2 characters long 749s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '9' because it was < 2 characters long 749s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '13' because it was < 2 characters long 749s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '15' because it was < 2 characters long 749s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '16' because it was < 2 characters long 749s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '17' because it was < 2 characters long 749s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '18' because it was < 2 characters long 749s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '19' because it was < 2 characters long 749s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '21' because it was < 2 characters long 749s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '25' because it was < 2 characters long 749s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '27' because it was < 2 characters long 749s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '29' because it was < 2 characters long 749s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '35' because it was < 2 characters long 749s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '40' because it was < 2 characters long 749s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '42' because it was < 2 characters long 749s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '43' because it was < 2 characters long 749s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '46' because it was < 2 characters long 749s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '61' because it was < 2 characters long 749s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '62' because it was < 2 characters long 749s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '66' because it was < 2 characters long 749s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '69' because it was < 2 characters long 749s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '80' because it was < 2 characters long 749s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '82' because it was < 2 characters long 749s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '85' because it was < 2 characters long 749s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '86' because it was < 2 characters long 749s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '88' because it was < 2 characters long 749s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '89' because it was < 2 characters long 749s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '93' because it was < 2 characters long 749s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '94' because it was < 2 characters long 749s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '97' because it was < 2 characters long 749s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '98' because it was < 2 characters long 749s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '101' because it was < 2 characters long 749s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '104' because it was < 2 characters long 749s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '106' because it was < 2 characters long 749s 107 reads; of these: 749s 107 (100.00%) were unpaired; of these: 749s 107 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s Read 50 alignments... 749s Read 100 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 0 alignments, 0 edits 749s --------------- 749s PASSED 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.2 749s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.1 749s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 13 749s Reference gaps introduced: 1 749s Read gaps introduced: 0 749s Rearrangements introduced: 0 749s Created read sampler 749s Sampling 142 reads 749s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 749s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 749s parsing sequence Sim.pm.1... 749s parsing sequence Sim.pm.2... 749s Parsed 94 reference bases 749s *** Run 89 of 100 749s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 1.43948009813009,1.3694020658262 --trim3 0 --rfg 24.063844379702,10.1184975309634 --score-min L,5.00069598250983,9.56233636047626 --gbar 9 -a --ma 26.3710004312615 --cp-min 7 -R 2 --norc --np 4 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 749s 142 reads; of these: 749s 142 (100.00%) were unpaired; of these: 749s 132 (92.96%) aligned 0 times 749s 3 (2.11%) aligned exactly 1 time 749s 7 (4.93%) aligned >1 times 749s 7.04% overall alignment rate 749s Read 50 alignments... 749s Read 100 alignments... 749s Read 150 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GC 749s GC 749s Processing line... 749s GC 749s GC 749s Processing line... 749s GC 749s GC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TTCA 749s TTCA 749s Processing line... 749s Processing line... 749s Processing line... 749s GG 749s GG 749s Processing line... 749s GG 749s GG 749s Processing line... 749s GG 749s GG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s ATGC 749s ATGC 749s Processing line... 749s CGT 749s CGT 749s Processing line... 749s CGT 749s CGT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s ATG 749s ATG 749s Processing line... 749s ATG 749s ATG 749s Processing line... 749s ATG 749s ATG 749s Processing line... 749s GATTCAAT 749s GATTCAAT 749s Processing line... 749s TT 749s TT 749s Processing line... 749s TT 749s TT 749s Processing line... 749s TT 749s TT 749s Processing line... 749s TT 749s TT 749s Processing line... 749s TT 749s TT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CCGAA 749s CCGAA 749s Processing line... 749s CCGAA 749s CCGAA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CCT 749s CCT 749s Processing line... 749s CCT 749s CCT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 23 alignments, 0 edits 749s --------------- 749s PASSED 749s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 749s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 1.43948009813009,1.3694020658262 --trim3 0 --rfg 24.063844379702,10.1184975309634 --score-min L,5.00069598250983,9.56233636047626 --gbar 9 -a --ma 26.3710004312615 --cp-min 7 -R 2 --norc --np 4 --qseq -p 3 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 749s 142 reads; of these: 749s 142 (100.00%) were unpaired; of these: 749s 132 (92.96%) aligned 0 times 749s 3 (2.11%) aligned exactly 1 time 749s 7 (4.93%) aligned >1 times 749s 7.04% overall alignment rate 749s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 749s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 749s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 749s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 749s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 1.43948009813009,1.3694020658262 --trim3 0 --rfg 24.063844379702,10.1184975309634 --score-min L,5.00069598250983,9.56233636047626 --gbar 9 -a --ma 26.3710004312615 --cp-min 7 -R 2 --norc --np 4 --qseq -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_132_132_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_133_133_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_134_134_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_134_134_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_135_135_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_136_136_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_138_138_1/1; setting to 0 instead 749s Warning: skipping read 'R_1_1_1_138_138_1/1' because length (1) <= # seed mismatches (0) 749s Warning: skipping read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_139_139_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_140_140_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_141_141_1/1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 749s 142 reads; of these: 749s 142 (100.00%) were unpaired; of these: 749s 132 (92.96%) aligned 0 times 749s 3 (2.11%) aligned exactly 1 time 749s 7 (4.93%) aligned >1 times 749s 7.04% overall alignment rate 749s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.1 749s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.2 749s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 1 749s Reference gaps introduced: 1 749s Read gaps introduced: 1 749s Rearrangements introduced: 0 749s Created read sampler 749s Sampling 159 reads 749s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 749s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 749s parsing sequence Sim.pm.1... 749s *** Run 90 of 100 749s /usr/bin/bowtie2 --cp-ival 2 --local --rfg 22.5815565206261 --score-min L,1.52563250049891,9.38957848544893 --gbar 9 --mm --cp-min 3 --trim5 4 -i L,0.49572966393876,3.99387869959683 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 749s parsing sequence Sim.pm.2... 749s Parsed 94 reference bases 749s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '8' because it was < 2 characters long 749s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '11' because it was < 2 characters long 749s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '13' because it was < 2 characters long 749s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '19' because it was < 2 characters long 749s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '21' because it was < 2 characters long 749s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '22' because it was < 2 characters long 749s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '35' because it was < 2 characters long 749s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '39' because it was < 2 characters long 749s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '50' because it was < 2 characters long 749s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '55' because it was < 2 characters long 749s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '60' because it was < 2 characters long 749s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '70' because it was < 2 characters long 749s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '72' because it was < 2 characters long 749s Read 50 alignments... 749s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '82' because it was < 2 characters long 749s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '84' because it was < 2 characters long 749s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '93' because it was < 2 characters long 749s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '106' because it was < 2 characters long 749s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '112' because it was < 2 characters long 749s Warning: skipping mate #1 of read '114' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '114' because it was < 2 characters long 749s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '115' because it was < 2 characters long 749s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '119' because it was < 2 characters long 749s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '121' because it was < 2 characters long 749s Warning: skipping mate #1 of read '125' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '125' because it was < 2 characters long 749s Read 100 alignments... 749s Read 150 alignments... 749s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '134' because it was < 2 characters long 749s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '137' because it was < 2 characters long 749s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '148' because it was < 2 characters long 749s Warning: skipping mate #2 of read '150' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '150' because it was < 2 characters long 749s Read 200 alignments... 749s 159 reads; of these: 749s 149 (93.71%) were paired; of these: 749s 149 (100.00%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 0 (0.00%) aligned concordantly >1 times 749s ---- 749s 149 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 749s ---- 749s 149 pairs aligned 0 times concordantly or discordantly; of these: 749s 298 mates make up the pairs; of these: 749s 298 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 10 (6.29%) were unpaired; of these: 749s 10 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s Read 250 alignments... 749s Read 300 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing 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line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 0 alignments, 0 edits 749s --------------- 749s PASSED 749s ALSO checking that bowtie2 and bowtie2-align match up 749s /usr/bin/bowtie2 --cp-ival 2 --local --rfg 22.5815565206261 --score-min L,1.52563250049891,9.38957848544893 --gbar 9 --mm --cp-min 3 --trim5 4 -i L,0.49572966393876,3.99387869959683 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 749s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '8' because it was < 2 characters long 749s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '11' because it was < 2 characters long 749s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '13' because it was < 2 characters long 749s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '19' because it was < 2 characters long 749s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '21' because it was < 2 characters long 749s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '22' because it was < 2 characters long 749s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '35' because it was < 2 characters long 749s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '39' because it was < 2 characters long 749s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '50' because it was < 2 characters long 749s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '55' because it was < 2 characters long 749s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '60' because it was < 2 characters long 749s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '70' because it was < 2 characters long 749s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '72' because it was < 2 characters long 749s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '82' because it was < 2 characters long 749s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '84' because it was < 2 characters long 749s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '93' because it was < 2 characters long 749s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '106' because it was < 2 characters long 749s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '112' because it was < 2 characters long 749s Warning: skipping mate #1 of read '114' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '114' because it was < 2 characters long 749s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '115' because it was < 2 characters long 749s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '119' because it was < 2 characters long 749s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '121' because it was < 2 characters long 749s Warning: skipping mate #1 of read '125' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '125' because it was < 2 characters long 749s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '134' because it was < 2 characters long 749s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '137' because it was < 2 characters long 749s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '148' because it was < 2 characters long 749s Warning: skipping mate #2 of read '150' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '150' because it was < 2 characters long 749s 159 reads; of these: 749s 149 (93.71%) were paired; of these: 749s 149 (100.00%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 0 (0.00%) aligned concordantly >1 times 749s ---- 749s 149 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 749s ---- 749s 149 pairs aligned 0 times concordantly or discordantly; of these: 749s 298 mates make up the pairs; of these: 749s 298 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 10 (6.29%) were unpaired; of these: 749s 10 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 749s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 749s /usr/bin/bowtie2 --cp-ival 2 --local --rfg 22.5815565206261 --score-min L,1.52563250049891,9.38957848544893 --gbar 9 --mm --cp-min 3 --trim5 4 -i L,0.49572966393876,3.99387869959683 -f -p 2 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 749s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '8' because it was < 2 characters long 749s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '11' because it was < 2 characters long 749s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '13' because it was < 2 characters long 749s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '19' because it was < 2 characters long 749s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '21' because it was < 2 characters long 749s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '22' because it was < 2 characters long 749s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '35' because it was < 2 characters long 749s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '39' because it was < 2 characters long 749s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '50' because it was < 2 characters long 749s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '55' because it was < 2 characters long 749s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '60' because it was < 2 characters long 749s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '70' because it was < 2 characters long 749s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '72' because it was < 2 characters long 749s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '82' because it was < 2 characters long 749s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '84' because it was < 2 characters long 749s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '93' because it was < 2 characters long 749s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '106' because it was < 2 characters long 749s Warning: skipping mate #1 of read '112' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '112' because it was < 2 characters long 749s Warning: skipping mate #1 of read '114' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '114' because it was < 2 characters long 749s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '115' because it was < 2 characters long 749s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '119' because it was < 2 characters long 749s Warning: skipping mate #1 of read '121' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '121' because it was < 2 characters long 749s Warning: skipping mate #1 of read '125' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '125' because it was < 2 characters long 749s Warning: skipping mate #1 of read '134' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '134' because it was < 2 characters long 749s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '137' because it was < 2 characters long 749s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '148' because it was < 2 characters long 749s Warning: skipping mate #2 of read '150' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '150' because it was < 2 characters long 749s 159 reads; of these: 749s 149 (93.71%) were paired; of these: 749s 149 (100.00%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 0 (0.00%) aligned concordantly >1 times 749s ---- 749s 149 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 749s ---- 749s 149 pairs aligned 0 times concordantly or discordantly; of these: 749s 298 mates make up the pairs; of these: 749s 298 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 10 (6.29%) were unpaired; of these: 749s 10 (100.00%) aligned 0 times 749s 0 (0.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 0.00% overall alignment rate 749s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 749s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 749s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 749s Flattened IUPAC characters 749s *** Run 91 of 100 749s /usr/bin/bowtie2 -R 1 --cp-ival 1 --cp-min 6 --ma 12.3671496613918 -i S,2.61770926858545 --trim5 9 --gbar 1 --np 5 --rfg 40.6052497948735,2.77799714828364 --rdg 29.8560618207628,19.6004151301623 --score-min L,7.486671549439,4.13068314460482 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 749s Mutating sequence Sim.pm.1 749s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.2 749s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 6 749s Reference gaps introduced: 0 749s Read gaps introduced: 1 749s Rearrangements introduced: 1 749s Created read sampler 749s Sampling 60 reads 749s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 749s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 749s parsing sequence Sim.pm.1... 749s parsing sequence Sim.pm.2... 749s Parsed 94 reference bases 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 749s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '2' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 749s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '6' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 749s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '10' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 749s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '12' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 749s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '13' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 749s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '16' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 749s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '17' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 749s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '23' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 749s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '25' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 749s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '30' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 749s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '34' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 749s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '35' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 749s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '37' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 749s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '41' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 749s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '42' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 749s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '43' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 749s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '48' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 749s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '51' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 749s 60 reads; of these: 749s 60 (100.00%) were unpaired; of these: 749s 54 (90.00%) aligned 0 times 749s 2 (3.33%) aligned exactly 1 time 749s 4 (6.67%) aligned >1 times 749s 10.00% overall alignment rate 749s Read 50 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TG 749s TG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GTCA 749s GTCA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s ACA 749s ACA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TTGGCGTC 749s TTGGCGTC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GAACATGGA 749s GAACATGGA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s ATCAT 749s ATCAT 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 6 alignments, 0 edits 749s --------------- 749s PASSED 749s ALSO checking that bowtie2 and bowtie2-align match up 749s /usr/bin/bowtie2 -R 1 --cp-ival 1 --cp-min 6 --ma 12.3671496613918 -i S,2.61770926858545 --trim5 9 --gbar 1 --np 5 --rfg 40.6052497948735,2.77799714828364 --rdg 29.8560618207628,19.6004151301623 --score-min L,7.486671549439,4.13068314460482 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 749s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '2' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 749s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '6' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 749s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '10' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 749s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '12' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 749s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '13' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 749s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '16' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 749s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '17' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 749s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '23' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 749s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '25' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 749s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '30' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 749s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '34' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 749s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '35' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 749s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '37' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 749s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '41' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 749s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '42' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 749s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '43' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 749s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '48' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 749s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '51' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 749s 60 reads; of these: 749s 60 (100.00%) were unpaired; of these: 749s 54 (90.00%) aligned 0 times 749s 2 (3.33%) aligned exactly 1 time 749s 4 (6.67%) aligned >1 times 749s 10.00% overall alignment rate 749s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 749s /usr/bin/bowtie2 -R 1 --cp-ival 1 --cp-min 6 --ma 12.3671496613918 -i S,2.61770926858545 --trim5 9 --gbar 1 --np 5 --rfg 40.6052497948735,2.77799714828364 --rdg 29.8560618207628,19.6004151301623 --score-min L,7.486671549439,4.13068314460482 -r -p 2 -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 749s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 749s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '2' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 749s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '6' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 749s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '10' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 749s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '12' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 749s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '13' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 749s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '16' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 749s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '17' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 749s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '23' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 749s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '25' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 749s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '30' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 749s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '34' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 749s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '35' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 749s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '37' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 749s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '41' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 749s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '42' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 749s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '43' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 749s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '48' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 749s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 749s Warning: skipping read '51' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 749s 60 reads; of these: 749s 60 (100.00%) were unpaired; of these: 749s 54 (90.00%) aligned 0 times 749s 2 (3.33%) aligned exactly 1 time 749s 4 (6.67%) aligned >1 times 749s 10.00% overall alignment rate 749s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 749s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 749s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.1 749s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.2 749s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 12 749s Reference gaps introduced: 0 749s Read gaps introduced: 0 749s Rearrangements introduced: 0 749s Created read sampler 749s Sampling 146 reads 749s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 749s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 749s parsing sequence Sim.pm.1... 749s *** Run 92 of 100 749s /usr/bin/bowtie2 -R 3 --cp-min 5 --np 4 --cp-ival 1 --mp 8.87957971438965,6.79862992460073 --nofw --rfg 31.9495840318104,9.12434432635516 --rdg 28.5480813587024,8.92552523858363 --score-min L,4.02278577160872,1.6556421018809 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw 749s parsing sequence Sim.pm.2... 749s Parsed 94 reference bases 749s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 749s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '21' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 749s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '23' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 749s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '27' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 749s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '31' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 749s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '34' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 749s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '54' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 749s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '64' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 749s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '86' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 749s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '110' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 749s 146 reads; of these: 749s 146 (100.00%) were unpaired; of these: 749s 130 (89.04%) aligned 0 times 749s 7 (4.79%) aligned exactly 1 time 749s 9 (6.16%) aligned >1 times 749s 10.96% overall alignment rate 749s Read 50 alignments... 749s Read 100 alignments... 749s Read 150 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CAA 749s CAA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s AACATG 749s AACATG 749s Processing line... 749s GG 749s GG 749s /usr/bin/bowtie2 -R 3 --cp-min 5 --np 4 --cp-ival 1 --mp 8.87957971438965,6.79862992460073 --nofw --rfg 31.9495840318104,9.12434432635516 --rdg 28.5480813587024,8.92552523858363 --score-min L,4.02278577160872,1.6556421018809 -r -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GG 749s GG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TGGATTCAA 749s TGGATTCAA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CATGAACATGGATTC 749s CATGAACATGGATTC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s AT 749s AT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CAT 749s CAT 749s Processing line... 749s Processing line... 749s Processing line... 749s ATGC 749s ATGC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s ATGAACATGGATT 749s ATGAACATGGATT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TTGG 749s TTGG 749s Processing line... 749s ACCTG 749s ACCTG 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CC 749s CC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TGA 749s TGA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CAT 749s CAT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TCAATC 749s TCAATC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 16 alignments, 0 edits 749s --------------- 749s PASSED 749s ALSO checking that bowtie2 and bowtie2-align match up 749s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 749s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '21' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 749s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '23' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 749s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '27' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 749s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '31' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 749s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '34' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 749s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '54' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 749s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '64' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 749s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '86' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 749s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '110' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 749s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 749s 146 reads; of these: 749s 146 (100.00%) were unpaired; of these: 749s 130 (89.04%) aligned 0 times 749s 7 (4.79%) aligned exactly 1 time 749s 9 (6.16%) aligned >1 times 749s 10.96% overall alignment rate 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.1 749s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.2 749s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 10 749s Reference gaps introduced: 0 749s Read gaps introduced: 0 749s Rearrangements introduced: 1 749s Created read sampler 749s Sampling 114 reads 749s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 749s *** Run 93 of 100 749s /usr/bin/bowtie2 --cp-min 2 --ma 21.8548342937887 -R 3 --np 3 --cp-ival 1 --n-ceil 0.331976255270644,1.17230903550343 --mp 6.19337318811413,1.87685642742216 --gbar 3 --score-min L,8.96674564349157,5.21778521710622 --rdg 23.5776330642862,1.82270414704916 -a -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 749s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 749s parsing sequence Sim.pm.1... 749s parsing sequence Sim.pm.2... 749s Parsed 94 reference bases 749s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 749s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 749s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '20' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 749s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '22' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 749s Warning: skipping read '61' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '61' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 749s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 749s Warning: skipping read '97' because it was < 2 characters long 749s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 749s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 749s Read 50 alignments... 749s 114 reads; of these: 749s 114 (100.00%) were unpaired; of these: 749s 89 (78.07%) aligned 0 times 749s 2 (1.75%) aligned exactly 1 time 749s 23 (20.18%) aligned >1 times 749s 21.93% overall alignment rate 749s Read 100 alignments... 749s Read 150 alignments... 749s Read 200 alignments... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TTGGCGTC 749s TTGGCGTC 749s Processing line... 749s TTGGCGTC 749s TTGGCGTC 749s Processing line... 749s CATGGA 749s CATGGA 749s Processing line... 749s TT 749s TT 749s Processing line... 749s TT 749s TT 749s Processing line... 749s AA 749s AA 749s Processing line... 749s TT 749s TT 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s TT 749s TT 749s Processing line... 749s AA 749s AA 749s Processing line... 749s TT 749s TT 749s Processing line... 749s AA 749s AA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TCAACA 749s TCAACA 749s Processing line... 749s TCAACA 749s TCAACA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s TT 749s TT 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s TT 749s TT 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s AA 749s AA 749s Processing line... 749s TT 749s TT 749s Processing line... 749s TT 749s TT 749s Processing line... 749s TT 749s TT 749s Processing line... 749s Processing line... 749s Processing line... 749s TCA 749s TCA 749s Processing line... 749s TGA 749s TGA 749s Processing line... 749s TCA 749s TCA 749s Processing line... 749s TCA 749s TCA 749s Processing line... 749s TCA 749s TCA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s AACAC 749s AACAC 749s Processing line... 749s AACAC 749s AACAC 749s Processing line... 749s AACAC 749s AACAC 749s Processing line... 749s Processing line... 749s Processing line... 749s GGC 749s GGC 749s Processing line... 749s GGC 749s GGC 749s Processing line... 749s Processing line... 749s TC 749s TC 749s Processing line... 749s TC 749s TC 749s Processing line... 749s GA 749s GA 749s Processing line... 749s TC 749s TC 749s Processing line... 749s GA 749s GA 749s Processing line... 749s GA 749s GA 749s Processing line... 749s GA 749s GA 749s Processing line... 749s TC 749s TC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s GT 749s GT 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s GT 749s GT 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s GG 749s GG 749s Processing line... 749s CC 749s CC 749s Processing line... 749s CC 749s CC 749s Processing line... 749s GG 749s GG 749s Processing line... 749s CC 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Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s GT 749s GT 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s GT 749s GT 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s Processing line... 749s AC 749s AC 749s Processing line... 749s GT 749s GT 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s GT 749s GT 749s Processing line... 749s AC 749s AC 749s Processing line... 749s AC 749s AC 749s Processing line... 749s Processing line... 749s TTT 749s TTT 749s Processing line... 749s AAA 749s AAA 749s Processing line... 749s AAA 749s AAA 749s Processing line... 749s Processing line... 749s CCCGA 749s CCCGA 749s Processing line... 749s CCCGA 749s CCCGA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CAC 749s CAC 749s Processing line... 749s CAC 749s CAC 749s Processing line... 749s CAC 749s CAC 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CCT 749s CCT 749s Processing line... 749s CCT 749s CCT 749s Processing line... 749s Processing line... 749s CGTCA 749s CGTCA 749s Processing line... 749s CGTCA 749s CGTCA 749s Processing line... 749s Processing line... 749s TAA 749s TAA 749s Processing line... 749s TTGGCGTCA 749s TTGGCGTCA 749s Processing line... 749s TTGGCGTCA 749s TTGGCGTCA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s CCT 749s CCT 749s Processing line... 749s CCT 749s CCT 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s TG 749s TG 749s Processing line... 749s CA 749s CA 749s Processing line... 749s TG 749s TG 749s Processing line... 749s CA 749s CA 749s Processing line... 749s TG 749s TG 749s Processing line... 749s CA 749s CA 749s Processing line... 749s CA 749s CA 749s Processing line... 749s TG 749s TG 749s Processing line... 749s CA 749s CA 749s Processing line... 749s CA 749s CA 749s Processing line... 749s TG 749s TG 749s Processing line... 749s CA 749s CA 749s Processing line... 749s CA 749s CA 749s Processing line... 749s CA 749s CA 749s Processing line... 749s CA 749s CA 749s Processing line... 749s TG 749s TG 749s Processing line... 749s CA 749s CA 749s Processing line... 749s TG 749s TG 749s Processing line... 749s ACA 749s ACA 749s Processing line... 749s ACA 749s ACA 749s Processing line... 749s ACA 749s ACA 749s Processing line... 749s ACA 749s ACA 749s Processing line... 749s ACA 749s ACA 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s Processing line... 749s --- Summary --- 749s Read 1 reference strings 749s Checked 146 alignments, 0 edits 749s --------------- 749s PASSED 749s Flattened IUPAC characters 749s Mutating sequence Sim.pm.1 749s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutating sequence Sim.pm.2 749s Introducing 5 SNPs, 1/0 ref/read gaps, and 1 rearrangements 749s Finished SNPs 749s Finished ref gaps 749s Finished read gaps 749s Mutated reference genome to subject genome 749s SNPs introduced: 5 749s Reference gaps introduced: 1 749s Read gaps introduced: 0 749s Rearrangements introduced: 1 749s Created read sampler 749s Sampling 69 reads 749s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 749s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 749s parsing sequence Sim.pm.1... 749s parsing sequence Sim.pm.2... 749s Parsed 94 reference bases 749s *** Run 94 of 100 749s /usr/bin/bowtie2 --score-min L,8.47342578752022,4.73817936226039 --rfg 42.1131270530707 --norc --mp 8.23368152084897,1.12339565925702 --cp-min 3 --cp-ival 3 --local --n-ceil 0.102498110482627,0.959116444468917 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 749s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '13' because it was < 2 characters long 749s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #1 of read '32' because it was < 2 characters long 749s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 749s Warning: skipping mate #2 of read '36' because it was < 2 characters long 749s Read 50 alignments... 749s Read 100 alignments... 749s 69 reads; of these: 749s 69 (100.00%) were paired; of these: 749s 69 (100.00%) aligned concordantly 0 times 749s 0 (0.00%) aligned concordantly exactly 1 time 749s 0 (0.00%) aligned concordantly >1 times 749s ---- 749s 69 pairs aligned concordantly 0 times; of these: 749s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 69 pairs aligned 0 times concordantly or discordantly; of these: 750s 138 mates make up the pairs; of these: 750s 138 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 0.00% overall alignment rate 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s --- Summary --- 750s Read 1 reference strings 750s Checked 0 alignments, 0 edits 750s --------------- 750s PASSED 750s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 750s /usr/bin/bowtie2 --score-min L,8.47342578752022,4.73817936226039 --rfg 42.1131270530707 --norc --mp 8.23368152084897,1.12339565925702 --cp-min 3 --cp-ival 3 --local --n-ceil 0.102498110482627,0.959116444468917 -q -p 2 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 750s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '13' because it was < 2 characters long 750s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '32' because it was < 2 characters long 750s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '36' because it was < 2 characters long 750s 69 reads; of these: 750s 69 (100.00%) were paired; of these: 750s 69 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 69 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 69 pairs aligned 0 times concordantly or discordantly; of these: 750s 138 mates make up the pairs; of these: 750s 138 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 0.00% overall alignment rate 750s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 750s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 750s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 750s Flattened IUPAC characters 750s Mutating sequence Sim.pm.1 750s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutating sequence Sim.pm.2 750s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutated reference genome to subject genome 750s SNPs introduced: 4 750s Reference gaps introduced: 0 750s Read gaps introduced: 1 750s Rearrangements introduced: 1 750s Created read sampler 750s Sampling 192 reads 750s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 750s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 750s parsing sequence Sim.pm.1... 750s parsing sequence Sim.pm.2... 750s Parsed 94 reference bases 750s *** Run 95 of 100 750s /usr/bin/bowtie2 --score-min L,5.05329378067049,9.8166702689682 --rfg 25.426899437926,6.62534976990648 -i S,1.0852708989978 --nofw --ma 28.4373984584486 --mp 9.32434052534818,9.04075334615262 --cp-min 10 --cp-ival 5 --n-ceil 0.560753823101556,1.02282897426768 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq 750s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 750s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 750s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '31' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 750s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '34' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 750s Warning: skipping read '98' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '98' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 750s Warning: skipping read '100' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '100' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 750s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '142' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 750s Warning: skipping read '150' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '150' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 750s Read 50 alignments... 750s 192 reads; of these: 750s 192 (100.00%) were unpaired; of these: 750s 174 (90.62%) aligned 0 times 750s 5 (2.60%) aligned exactly 1 time 750s 13 (6.77%) aligned >1 times 750s 9.38% overall alignment rate 750s Read 100 alignments... 750s Read 150 alignments... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s AC 750s AC 750s Processing line... 750s TT 750s TT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CAAT 750s CAAT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GC 750s GC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s ATCATAACACAT 750s ATCATAACACAT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s TT 750s TT 750s Processing line... 750s TTG 750s TTG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CATG 750s CATG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GT 750s GT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CAA 750s CAA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CATGG 750s CATGG 750s Processing line... 750s Processing line... 750s Processing line... 750s TCA 750s TCA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CA 750s CA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s ATG 750s ATG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GGCGTCAACA 750s GGCGTCAACA 750s Processing line... 750s Processing line... 750s Processing line... 750s GGATTCAATC 750s GGATTCAATC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s ATCATAACACA 750s ATCATAACACA 750s Processing line... 750s Processing line... 750s Processing line... 750s GT 750s GT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s --- Summary --- 750s Read 1 reference strings 750s Checked 18 alignments, 0 edits 750s --------------- 750s PASSED 750s ALSO checking that bowtie2 and bowtie2-align match up 750s /usr/bin/bowtie2 --score-min L,5.05329378067049,9.8166702689682 --rfg 25.426899437926,6.62534976990648 -i S,1.0852708989978 --nofw --ma 28.4373984584486 --mp 9.32434052534818,9.04075334615262 --cp-min 10 --cp-ival 5 --n-ceil 0.560753823101556,1.02282897426768 -q -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 750s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 750s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 750s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '31' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 750s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '34' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 750s Warning: skipping read '98' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '98' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 750s Warning: skipping read '100' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '100' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 750s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '142' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 750s Warning: skipping read '150' because length (1) <= # seed mismatches (0) 750s Warning: skipping read '150' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 750s 192 reads; of these: 750s 192 (100.00%) were unpaired; of these: 750s 174 (90.62%) aligned 0 times 750s 5 (2.60%) aligned exactly 1 time 750s 13 (6.77%) aligned >1 times 750s 9.38% overall alignment rate 750s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 750s Flattened IUPAC characters 750s Mutating sequence Sim.pm.2 750s Introducing 4 SNPs, 1/2 ref/read gaps, and 0 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutating sequence Sim.pm.1 750s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutated reference genome to subject genome 750s SNPs introduced: 6 750s Reference gaps introduced: 2 750s Read gaps introduced: 2 750s Rearrangements introduced: 1 750s Created read sampler 750s Sampling 22 reads 750s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.qseq & /tmp/Sim.pm.WCUbbuUs_2.qseq 750s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 750s parsing sequence Sim.pm.1... 750s parsing sequence Sim.pm.2... 750s *** Run 96 of 100 750s /usr/bin/bowtie2 --nofw --ma 11.8774410102435 --cp-ival 2 -D 6 --cp-min 2 --score-min L,3.72796117974292,9.09989233570679 --trim5 8 --qseq -x /tmp/Sim.pm.WCUbbuUs /tmp/Sim.pm.WCUbbuUs_1.qseq 750s Parsed 94 reference bases 750s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 750s 22 reads; of these: 750s 22 (100.00%) were unpaired; of these: 750s 21 (95.45%) aligned 0 times 750s 1 (4.55%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 4.55% overall alignment rate 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s TGGATTCAATCATA 750s TGGATTCAATCATA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s /usr/bin/bowtie2 --nofw --ma 11.8774410102435 --cp-ival 2 -D 6 --cp-min 2 --score-min L,3.72796117974292,9.09989233570679 --trim5 8 --qseq -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder /tmp/Sim.pm.WCUbbuUs_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s --- Summary --- 750s Read 1 reference strings 750s Checked 1 alignments, 0 edits 750s --------------- 750s PASSED 750s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 750s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 750s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 750s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 750s 22 reads; of these: 750s 22 (100.00%) were unpaired; of these: 750s 21 (95.45%) aligned 0 times 750s 1 (4.55%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 4.55% overall alignment rate 750s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 750s Flattened IUPAC characters 750s Mutating sequence Sim.pm.2 750s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutating sequence Sim.pm.1 750s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutated reference genome to subject genome 750s SNPs introduced: 5 750s Reference gaps introduced: 0 750s Read gaps introduced: 1 750s Rearrangements introduced: 1 750s Created read sampler 750s Sampling 98 reads 750s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fastq & /tmp/Sim.pm.WCUbbuUs_2.fastq 750s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 750s parsing sequence Sim.pm.1... 750s parsing sequence Sim.pm.2... 750s Parsed 94 reference bases 750s *** Run 97 of 100 750s /usr/bin/bowtie2 --cp-min 4 -R 4 -k 9 -i C,1.40025917627943,7.6010016035685 --trim5 7 --cp-ival 2 --n-ceil 0.50483295363877,0.585351283780699 --mp 9.66991480623501,8.28910686195553 --score-min L,1.28812492382276,4.20649663617472 --rfg 23.7479035605545,7.56868581815543 --rdg 15.7162863122692,11.4584108609543 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 750s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '9' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 750s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '17' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 750s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '20' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 750s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '25' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 750s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '29' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 750s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '33' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 750s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 750s Warning: skipping read '38' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 750s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 750s Warning: skipping read '64' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 750s Read 50 alignments... 750s Read 100 alignments... 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 750s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '69' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 750s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '75' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 750s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '78' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 750s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '85' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 750s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '88' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 750s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '98' because it was < 2 characters long 750s 98 reads; of these: 750s 83 (84.69%) were paired; of these: 750s 83 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 83 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 83 pairs aligned 0 times concordantly or discordantly; of these: 750s 166 mates make up the pairs; of these: 750s 159 (95.78%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 7 (4.22%) aligned >1 times 750s 15 (15.31%) were unpaired; of these: 750s 14 (93.33%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 1 (6.67%) aligned >1 times 750s 4.42% overall alignment rate 750s Read 150 alignments... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GCGTCA 750s GCGTCA 750s Processing line... 750s GCGTCA 750s GCGTCA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GTCA 750s GTCA 750s Processing line... 750s GTCA 750s GTCA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s /usr/bin/bowtie2 --cp-min 4 -R 4 -k 9 -i C,1.40025917627943,7.6010016035685 --trim5 7 --cp-ival 2 --n-ceil 0.50483295363877,0.585351283780699 --mp 9.66991480623501,8.28910686195553 --score-min L,1.28812492382276,4.20649663617472 --rfg 23.7479035605545,7.56868581815543 --rdg 15.7162863122692,11.4584108609543 -q -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CACC 750s CACC 750s Processing line... 750s CACC 750s CACC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GA 750s GA 750s Processing line... 750s GA 750s GA 750s Processing line... 750s TC 750s TC 750s Processing line... 750s TC 750s TC 750s Processing line... 750s TC 750s TC 750s Processing line... 750s TC 750s TC 750s Processing line... 750s GA 750s GA 750s Processing line... 750s GA 750s GA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s ACACCTG 750s ACACCTG 750s Processing line... 750s ACACCTG 750s ACACCTG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s GTCAA 750s GTCAA 750s Processing line... 750s GTCAA 750s GTCAA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CGA 750s CGA 750s Processing line... 750s CGA 750s CGA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s AACACCT 750s AACACCT 750s Processing line... 750s AACACCT 750s AACACCT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s --- Summary --- 750s Read 1 reference strings 750s Checked 22 alignments, 0 edits 750s --------------- 750s PASSED 750s ALSO checking that bowtie2 and bowtie2-align match up 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 750s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '9' because it was < 2 characters long 750s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 750s /usr/bin/bowtie2 --cp-min 4 -R 4 -k 9 -i C,1.40025917627943,7.6010016035685 --trim5 7 --cp-ival 2 --n-ceil 0.50483295363877,0.585351283780699 --mp 9.66991480623501,8.28910686195553 --score-min L,1.28812492382276,4.20649663617472 --rfg 23.7479035605545,7.56868581815543 --rdg 15.7162863122692,11.4584108609543 -q -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fastq -2 /tmp/Sim.pm.WCUbbuUs_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 750s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '17' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 750s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '20' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 750s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '25' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 750s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '29' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 750s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '33' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 750s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 750s Warning: skipping read '38' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 750s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 750s Warning: skipping read '64' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 750s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '69' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 750s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '75' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 750s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '78' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 750s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '85' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 750s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '88' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 750s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '98' because it was < 2 characters long 750s 98 reads; of these: 750s 83 (84.69%) were paired; of these: 750s 83 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 83 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 83 pairs aligned 0 times concordantly or discordantly; of these: 750s 166 mates make up the pairs; of these: 750s 159 (95.78%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 7 (4.22%) aligned >1 times 750s 15 (15.31%) were unpaired; of these: 750s 14 (93.33%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 1 (6.67%) aligned >1 times 750s 4.42% overall alignment rate 750s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 750s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '9' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 750s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '17' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 750s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '33' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 750s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 750s Warning: skipping read '38' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 750s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 750s Warning: skipping read '64' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 750s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '69' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 750s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '75' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 750s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '78' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 750s Warning: skipping mate #2 of read '85' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '85' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 750s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '88' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 750s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '20' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 750s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '25' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 750s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '29' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 750s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '98' because it was < 2 characters long 750s 98 reads; of these: 750s 83 (84.69%) were paired; of these: 750s 83 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 83 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 83 pairs aligned 0 times concordantly or discordantly; of these: 750s 166 mates make up the pairs; of these: 750s 159 (95.78%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 7 (4.22%) aligned >1 times 750s 15 (15.31%) were unpaired; of these: 750s 14 (93.33%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 1 (6.67%) aligned >1 times 750s 4.42% overall alignment rate 750s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 750s Flattened IUPAC characters 750s Mutating sequence Sim.pm.2 750s Introducing 3 SNPs, 1/1 ref/read gaps, and 1 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutating sequence Sim.pm.1 750s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutated reference genome to subject genome 750s SNPs introduced: 9 750s Reference gaps introduced: 2 750s Read gaps introduced: 1 750s Rearrangements introduced: 1 750s Created read sampler 750s Sampling 89 reads 750s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 750s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 750s parsing sequence Sim.pm.1... 750s parsing sequence Sim.pm.2... 750s Parsed 94 reference bases 750s *** Run 98 of 100 750s /usr/bin/bowtie2 --cp-min 8 --norc -M 2 --local --cp-ival 1 --n-ceil 0.674381684196388,1.20898356184531 --trim3 2 --gbar 3 --rdg 30.7962653188419 --score-min L,3.05726662923939,4.20964139644965 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 750s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 750s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '8' because it was < 2 characters long 750s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '19' because it was < 2 characters long 750s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '31' because it was < 2 characters long 750s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '37' because it was < 2 characters long 750s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '38' because it was < 2 characters long 750s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '40' because it was < 2 characters long 750s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '58' because it was < 2 characters long 750s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '62' because it was < 2 characters long 750s Read 50 alignments... 750s Read 100 alignments... 750s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '65' because it was < 2 characters long 750s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '70' because it was < 2 characters long 750s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '71' because it was < 2 characters long 750s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '76' because it was < 2 characters long 750s 89 reads; of these: 750s 83 (93.26%) were paired; of these: 750s 83 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 83 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 83 pairs aligned 0 times concordantly or discordantly; of these: 750s 166 mates make up the pairs; of these: 750s 166 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 6 (6.74%) were unpaired; of these: 750s 6 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 0.00% overall alignment rate 750s Read 150 alignments... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s /usr/bin/bowtie2 --cp-min 8 --norc -M 2 --local --cp-ival 1 --n-ceil 0.674381684196388,1.20898356184531 --trim3 2 --gbar 3 --rdg 30.7962653188419 --score-min L,3.05726662923939,4.20964139644965 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s --- Summary --- 750s Read 1 reference strings 750s Checked 0 alignments, 0 edits 750s --------------- 750s PASSED 750s ALSO checking that bowtie2 and bowtie2-align match up 750s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 750s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '8' because it was < 2 characters long 750s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '19' because it was < 2 characters long 750s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '31' because it was < 2 characters long 750s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '37' because it was < 2 characters long 750s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '38' because it was < 2 characters long 750s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '40' because it was < 2 characters long 750s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '58' because it was < 2 characters long 750s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '62' because it was < 2 characters long 750s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '65' because it was < 2 characters long 750s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '70' because it was < 2 characters long 750s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '71' because it was < 2 characters long 750s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '76' because it was < 2 characters long 750s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 750s 89 reads; of these: 750s 83 (93.26%) were paired; of these: 750s 83 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 83 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 83 pairs aligned 0 times concordantly or discordantly; of these: 750s 166 mates make up the pairs; of these: 750s 166 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 6 (6.74%) were unpaired; of these: 750s 6 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 0.00% overall alignment rate 750s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 750s /usr/bin/bowtie2 --cp-min 8 --norc -M 2 --local --cp-ival 1 --n-ceil 0.674381684196388,1.20898356184531 --trim3 2 --gbar 3 --rdg 30.7962653188419 --score-min L,3.05726662923939,4.20964139644965 -r -p 4 -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als 750s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 750s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '8' because it was < 2 characters long 750s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '19' because it was < 2 characters long 750s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '31' because it was < 2 characters long 750s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '37' because it was < 2 characters long 750s Warning: skipping mate #1 of read '38' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '38' because it was < 2 characters long 750s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '40' because it was < 2 characters long 750s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '58' because it was < 2 characters long 750s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '62' because it was < 2 characters long 750s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '65' because it was < 2 characters long 750s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '70' because it was < 2 characters long 750s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '71' because it was < 2 characters long 750s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '76' because it was < 2 characters long 750s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.px.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.als.sorted 750s 89 reads; of these: 750s 83 (93.26%) were paired; of these: 750s 83 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 83 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 83 pairs aligned 0 times concordantly or discordantly; of these: 750s 166 mates make up the pairs; of these: 750s 166 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 6 (6.74%) were unpaired; of these: 750s 6 (100.00%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 0.00% overall alignment rate 750s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.WCUbbuUs.debug.als | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.debug.als.sorted 750s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als.sorted /tmp/Sim.pm.WCUbbuUs.px.als.sorted 750s Flattened IUPAC characters 750s Mutating sequence Sim.pm.2 750s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutating sequence Sim.pm.1 750s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 750s Finished SNPs 750s Finished ref gaps 750s Finished read gaps 750s Mutated reference genome to subject genome 750s SNPs introduced: 3 750s Reference gaps introduced: 1 750s Read gaps introduced: 0 750s Rearrangements introduced: 0 750s Created read sampler 750s Sampling 61 reads 750s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.raw & /tmp/Sim.pm.WCUbbuUs_2.raw 750s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 750s parsing sequence Sim.pm.1... 750s parsing sequence Sim.pm.2... 750s Parsed 94 reference bases 750s *** Run 99 of 100 750s /usr/bin/bowtie2 --score-min L,4.01936615195411,3.96470682043586 --rdg 49.6265103338535,18.0704383864008 --np 3 --nofw --mp 6.24222434665499,2.71412593764286 --cp-min 2 --cp-ival 1 --n-ceil 1.44287346636143,1.4348546480586 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 750s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #1 of read '32' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 750s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 750s Warning: skipping mate #2 of read '54' because it was < 2 characters long 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 750s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 750s 61 reads; of these: 750s 61 (100.00%) were paired; of these: 750s 61 (100.00%) aligned concordantly 0 times 750s 0 (0.00%) aligned concordantly exactly 1 time 750s 0 (0.00%) aligned concordantly >1 times 750s ---- 750s 61 pairs aligned concordantly 0 times; of these: 750s 0 (0.00%) aligned discordantly 1 time 750s ---- 750s 61 pairs aligned 0 times concordantly or discordantly; of these: 750s 122 mates make up the pairs; of these: 750s 114 (93.44%) aligned 0 times 750s 0 (0.00%) aligned exactly 1 time 750s 8 (6.56%) aligned >1 times 750s 6.56% overall alignment rate 750s Read 50 alignments... 750s Read 100 alignments... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CCGA 750s CCGA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s TG 750s TG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s TTG 750s TTG 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s ACACCT 750s ACACCT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s CCCGAA 750s CCCGAA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s AC 750s AC 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s TA 750s TA 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s TT 750s TT 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s Processing line... 750s --- Summary --- 750s Read 1 reference strings 750s Checked 8 alignments, 0 edits 750s --------------- 750s PASSED 750s ALSO checking that bowtie2 and bowtie2-align match up 750s /usr/bin/bowtie2 --score-min L,4.01936615195411,3.96470682043586 --rdg 49.6265103338535,18.0704383864008 --np 3 --nofw --mp 6.24222434665499,2.71412593764286 --cp-min 2 --cp-ival 1 --n-ceil 1.44287346636143,1.4348546480586 -r -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.als 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 751s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '32' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 751s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '54' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 751s 61 reads; of these: 751s 61 (100.00%) were paired; of these: 751s 61 (100.00%) aligned concordantly 0 times 751s 0 (0.00%) aligned concordantly exactly 1 time 751s 0 (0.00%) aligned concordantly >1 times 751s ---- 751s 61 pairs aligned concordantly 0 times; of these: 751s 0 (0.00%) aligned discordantly 1 time 751s ---- 751s 61 pairs aligned 0 times concordantly or discordantly; of these: 751s 122 mates make up the pairs; of these: 751s 114 (93.44%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 8 (6.56%) aligned >1 times 751s 6.56% overall alignment rate 751s diff -uw /tmp/Sim.pm.WCUbbuUs.als /tmp/Sim.pm.WCUbbuUs.debug.als 751s /usr/bin/bowtie2 --score-min L,4.01936615195411,3.96470682043586 --rdg 49.6265103338535,18.0704383864008 --np 3 --nofw --mp 6.24222434665499,2.71412593764286 --cp-min 2 --cp-ival 1 --n-ceil 1.44287346636143,1.4348546480586 -r -p 2 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.raw -2 /tmp/Sim.pm.WCUbbuUs_2.raw | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 751s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 751s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '32' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 751s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 751s Warning: skipping mate #2 of read '54' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 751s 61 reads; of these: 751s 61 (100.00%) were paired; of these: 751s 61 (100.00%) aligned concordantly 0 times 751s 0 (0.00%) aligned concordantly exactly 1 time 751s 0 (0.00%) aligned concordantly >1 times 751s ---- 751s 61 pairs aligned concordantly 0 times; of these: 751s 0 (0.00%) aligned discordantly 1 time 751s ---- 751s 61 pairs aligned 0 times concordantly or discordantly; of these: 751s 122 mates make up the pairs; of these: 751s 114 (93.44%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 8 (6.56%) aligned >1 times 751s 6.56% overall alignment rate 751s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 751s Flattened IUPAC characters 751s Mutating sequence Sim.pm.1 751s Introducing 6 SNPs, 2/0 ref/read gaps, and 1 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutating sequence Sim.pm.2 751s Introducing 7 SNPs, 0/1 ref/read gaps, and 4 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutated reference genome to subject genome 751s SNPs introduced: 13 751s Reference gaps introduced: 2 751s Read gaps introduced: 1 751s Rearrangements introduced: 5 751s Created read sampler 751s Sampling 17 reads 751s Dumping reads to temporary files /tmp/Sim.pm.WCUbbuUs_1.fasta & /tmp/Sim.pm.WCUbbuUs_2.fasta 751s Parsing FASTA file /tmp/Sim.pm.WCUbbuUs.fa... 751s parsing sequence Sim.pm.1... 751s parsing sequence Sim.pm.2... 751s Parsed 94 reference bases 751s *** Run 100 of 100 751s /usr/bin/bowtie2 --ma 20.2170393045285 --cp-ival 2 --cp-min 2 --rdg 34.5692426759683,9.12532599021341 --score-min L,5.05302685476247,9.78214201493285 --np 3 --trim5 6 -f -x /tmp/Sim.pm.WCUbbuUs -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta 751s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 751s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 751s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '3' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 751s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '13' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 751s 17 reads; of these: 751s 13 (76.47%) were paired; of these: 751s 13 (100.00%) aligned concordantly 0 times 751s 0 (0.00%) aligned concordantly exactly 1 time 751s 0 (0.00%) aligned concordantly >1 times 751s ---- 751s 13 pairs aligned concordantly 0 times; of these: 751s 0 (0.00%) aligned discordantly 1 time 751s ---- 751s 13 pairs aligned 0 times concordantly or discordantly; of these: 751s 26 mates make up the pairs; of these: 751s 26 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 4 (23.53%) were unpaired; of these: 751s 4 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s --- Summary --- 751s Read 1 reference strings 751s Checked 0 alignments, 0 edits 751s --------------- 751s PASSED 751s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 751s /usr/bin/bowtie2 --ma 20.2170393045285 --cp-ival 2 --cp-min 2 --rdg 34.5692426759683,9.12532599021341 --score-min L,5.05302685476247,9.78214201493285 --np 3 --trim5 6 -f -p 3 -x /tmp/Sim.pm.WCUbbuUs --reorder -1 /tmp/Sim.pm.WCUbbuUs_1.fasta -2 /tmp/Sim.pm.WCUbbuUs_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.WCUbbuUs.px.reord.als 751s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 751s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 751s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 751s Warning: skipping mate #1 of read '3' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 751s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '13' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 751s 17 reads; of these: 751s 13 (76.47%) were paired; of these: 751s 13 (100.00%) aligned concordantly 0 times 751s 0 (0.00%) aligned concordantly exactly 1 time 751s 0 (0.00%) aligned concordantly >1 times 751s ---- 751s 13 pairs aligned concordantly 0 times; of these: 751s 0 (0.00%) aligned discordantly 1 time 751s ---- 751s 13 pairs aligned 0 times concordantly or discordantly; of these: 751s 26 mates make up the pairs; of these: 751s 26 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 4 (23.53%) were unpaired; of these: 751s 4 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s diff -uw /tmp/Sim.pm.WCUbbuUs.debug.als /tmp/Sim.pm.WCUbbuUs.px.reord.als 751s Created DNA generator 751s N frac: 0.026 751s IUPAC frac: 0.009 751s AT/ACGT frac: 0.547 751s A/AT frac: 0.610 751s C/CG frac: 0.700 751s Generating 2 references 751s Generated reference 'Sim.pm.1' of untrimmed length 71, trimmed length 33 751s Generated reference 'Sim.pm.2' of untrimmed length 115, trimmed length 25 751s Wrote references to /tmp/Sim.pm.sD3XFvJi.fa 751s A: 15 751s C: 21 751s G: 7 751s M: 2 751s N: 2 751s T: 11 751s Executing: /usr/bin/bowtie2-build --bmax 1556 --threads 2 --offrate 5 --dcv 256 /tmp/Sim.pm.sD3XFvJi.fa /tmp/Sim.pm.sD3XFvJi 751s *** TEST CASE *** 751s Settings: 751s Output files: "/tmp/Sim.pm.sD3XFvJi.*.bt2" 751s Line rate: 6 (line is 64 bytes) 751s Lines per side: 1 (side is 64 bytes) 751s Offset rate: 5 (one in 32) 751s FTable chars: 10 751s Strings: unpacked 751s Max bucket size: 1556 751s Max bucket size, sqrt multiplier: default 751s Max bucket size, len divisor: 4294967294 751s Difference-cover sample period: 256 751s Endianness: little 751s Building a SMALL index Actual local endianness: little 751s Sanity checking: disabled 751s Assertions: disabled 751s Random seed: 0 751s Sizeofs: void*:8, int:4, long:8, size_t:8 751s Input files DNA, FASTA: 751s /tmp/Sim.pm.sD3XFvJi.fa 751s 751s Reading reference sizes 751s Time reading reference sizes: 00:00:00 751s Calculating joined length 751s Writing header 751s Reserving space for joined string 751s Joining reference sequences 751s Time to join reference sequences: 00:00:00 751s bmax according to bmax setting: 1556 751s Using parameters --bmax 1167 --dcv 256 751s Doing ahead-of-time memory usage test 751s Passed! Constructing with these parameters: --bmax 1167 --dcv 256 751s Constructing suffix-array element generator 751s Building DifferenceCoverSample 751s Building sPrime 751s Building sPrimeOrder 751s V-Sorting samples 751s V-Sorting samples time: 00:00:00 751s Allocating rank array 751s Ranking v-sort output 751s Ranking v-sort output time: 00:00:00 751s Invoking Larsson-Sadakane on ranks 751s Invoking Larsson-Sadakane on ranks time: 00:00:00 751s Sanity-checking and returning 751s Skipping building samples since text length 54 is less than bucket size: 1167 751s Converting suffix-array elements to index image 751s Allocating ftab, absorbFtab 751s Entering Ebwt loop 751s Getting block 1 of 1 751s No samples; assembling all-inclusive block 751s Sorting block of length 54 for bucket 1 751s (Using difference cover) 751s Sorting block time: 00:00:00 751s Returning block of 55 for bucket 1 751s Exited Ebwt loop 751s fchr[A]: 0 751s fchr[C]: 15 751s fchr[G]: 36 751s fchr[T]: 43 751s fchr[$]: 54 751s Exiting Ebwt::buildToDisk() 751s Returning from initFromVector 751s Wrote 4194611 bytes to primary EBWT file: /tmp/Sim.pm.sD3XFvJi.1.bt2.tmp 751s Wrote 12 bytes to secondary EBWT file: /tmp/Sim.pm.sD3XFvJi.2.bt2.tmp 751s Re-opening _in1 and _in2 as input streams 751s Returning from Ebwt constructor 751s Headers: 751s len: 54 751s bwtLen: 55 751s sz: 14 751s bwtSz: 14 751s lineRate: 6 751s offRate: 5 751s offMask: 0xffffffe0 751s ftabChars: 10 751s eftabLen: 20 751s eftabSz: 80 751s ftabLen: 1048577 751s ftabSz: 4194308 751s offsLen: 2 751s offsSz: 8 751s lineSz: 64 751s sideSz: 64 751s sideBwtSz: 48 751s sideBwtLen: 192 751s numSides: 1 751s numLines: 1 751s ebwtTotLen: 64 751s ebwtTotSz: 64 751s color: 0 751s reverse: 0 751s Total time for call to driver() for forward index: 00:00:00 751s Reading reference sizes 751s Time reading reference sizes: 00:00:00 751s Calculating joined length 751s Writing header 751s Reserving space for joined string 751s Joining reference sequences 751s Time to join reference sequences: 00:00:00 751s Time to reverse reference sequence: 00:00:00 751s bmax according to bmax setting: 1556 751s Using parameters --bmax 1167 --dcv 256 751s Doing ahead-of-time memory usage test 751s Passed! Constructing with these parameters: --bmax 1167 --dcv 256 751s Constructing suffix-array element generator 751s Building DifferenceCoverSample 751s Building sPrime 751s Building sPrimeOrder 751s V-Sorting samples 751s V-Sorting samples time: 00:00:00 751s Allocating rank array 751s Ranking v-sort output 751s Ranking v-sort output time: 00:00:00 751s Invoking Larsson-Sadakane on ranks 751s Invoking Larsson-Sadakane on ranks time: 00:00:00 751s Sanity-checking and returning 751s Skipping building samples since text length 54 is less than bucket size: 1167 751s Converting suffix-array elements to index image 751s Allocating ftab, absorbFtab 751s Entering Ebwt loop 751s Getting block 1 of 1 751s No samples; assembling all-inclusive block 751s Sorting block of length 54 for bucket 1 751s (Using difference cover) 751s Sorting block time: 00:00:00 751s Returning block of 55 for bucket 1 751s Exited Ebwt loop 751s fchr[A]: 0 751s fchr[C]: 15 751s fchr[G]: 36 751s fchr[T]: 43 751s fchr[$]: 54 751s Exiting Ebwt::buildToDisk() 751s Returning from initFromVector 751s Wrote 4194611 bytes to primary EBWT file: /tmp/Sim.pm.sD3XFvJi.rev.1.bt2.tmp 751s Wrote 12 bytes to secondary EBWT file: /tmp/Sim.pm.sD3XFvJi.rev.2.bt2.tmp 751s Re-opening _in1 and _in2 as input streams 751s Returning from Ebwt constructor 751s Headers: 751s len: 54 751s bwtLen: 55 751s sz: 14 751s bwtSz: 14 751s lineRate: 6 751s offRate: 5 751s offMask: 0xffffffe0 751s ftabChars: 10 751s eftabLen: 20 751s eftabSz: 80 751s ftabLen: 1048577 751s ftabSz: 4194308 751s offsLen: 2 751s offsSz: 8 751s lineSz: 64 751s sideSz: 64 751s sideBwtSz: 48 751s sideBwtLen: 192 751s numSides: 1 751s numLines: 1 751s ebwtTotLen: 64 751s ebwtTotSz: 64 751s color: 0 751s reverse: 1 751s Total time for backward call to driver() for mirror index: 00:00:00 751s Renaming /tmp/Sim.pm.sD3XFvJi.3.bt2.tmp to /tmp/Sim.pm.sD3XFvJi.3.bt2 751s Renaming /tmp/Sim.pm.sD3XFvJi.4.bt2.tmp to /tmp/Sim.pm.sD3XFvJi.4.bt2 751s Renaming /tmp/Sim.pm.sD3XFvJi.1.bt2.tmp to /tmp/Sim.pm.sD3XFvJi.1.bt2 751s Renaming /tmp/Sim.pm.sD3XFvJi.2.bt2.tmp to /tmp/Sim.pm.sD3XFvJi.2.bt2 751s Renaming /tmp/Sim.pm.sD3XFvJi.rev.1.bt2.tmp to /tmp/Sim.pm.sD3XFvJi.rev.1.bt2 751s Renaming /tmp/Sim.pm.sD3XFvJi.rev.2.bt2.tmp to /tmp/Sim.pm.sD3XFvJi.rev.2.bt2 751s Built nucleotide index '/tmp/Sim.pm.sD3XFvJi' 751s Flattened IUPAC characters 751s Mutating sequence Sim.pm.2 751s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutating sequence Sim.pm.1 751s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutated reference genome to subject genome 751s SNPs introduced: 7 751s Reference gaps introduced: 0 751s Read gaps introduced: 1 751s Rearrangements introduced: 0 751s Created read sampler 751s Sampling 26 reads 751s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 751s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 751s parsing sequence Sim.pm.1... 751s *** Run 1 of 100 751s /usr/bin/bowtie2 --cp-min 9 --ma 12.1706786521281 -M 4 --trim5 7 --np 2 --trim3 0 --n-ceil 1.4169350017046,1.22266842328329 --cp-ival 2 --score-min L,6.31603254743981,8.24191661531241 --rfg 36.7539200964771,10.6173279329542 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 751s parsing sequence Sim.pm.2... 751s Parsed 58 reference bases 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 751s 26 reads; of these: 751s 26 (100.00%) were unpaired; of these: 751s 25 (96.15%) aligned 0 times 751s 1 (3.85%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 3.85% overall alignment rate 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s CCTTAC 751s CCTTAC 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s --- Summary --- 751s Read 1 reference strings 751s Checked 1 alignments, 0 edits 751s --------------- 751s PASSED 751s ALSO checking that bowtie2 and bowtie2-align match up 751s /usr/bin/bowtie2 --cp-min 9 --ma 12.1706786521281 -M 4 --trim5 7 --np 2 --trim3 0 --n-ceil 1.4169350017046,1.22266842328329 --cp-ival 2 --score-min L,6.31603254743981,8.24191661531241 --rfg 36.7539200964771,10.6173279329542 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 751s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 751s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 751s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 751s 26 reads; of these: 751s 26 (100.00%) were unpaired; of these: 751s 25 (96.15%) aligned 0 times 751s 1 (3.85%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 3.85% overall alignment rate 751s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 751s Flattened IUPAC characters 751s Mutating sequence Sim.pm.2 751s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutating sequence Sim.pm.1 751s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutated reference genome to subject genome 751s SNPs introduced: 4 751s Reference gaps introduced: 0 751s Read gaps introduced: 0 751s Rearrangements introduced: 1 751s Created read sampler 751s Sampling 93 reads 751s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 751s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 751s parsing sequence Sim.pm.1... 751s parsing sequence Sim.pm.2... 751s Parsed 58 reference bases 751s *** Run 2 of 100 751s /usr/bin/bowtie2 --np 6 --norc -M 3 --cp-min 4 --gbar 8 --rfg 27.4582023988232 --score-min L,7.18656816466632,8.3949211978206 --mm --local --cp-ival 4 -N 0 -L26 --trim3 3 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '2' because it was < 2 characters long 751s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '8' because it was < 2 characters long 751s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '23' because it was < 2 characters long 751s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '25' because it was < 2 characters long 751s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '27' because it was < 2 characters long 751s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '31' because it was < 2 characters long 751s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '38' because it was < 2 characters long 751s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '46' because it was < 2 characters long 751s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '47' because it was < 2 characters long 751s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '55' because it was < 2 characters long 751s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '64' because it was < 2 characters long 751s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '67' because it was < 2 characters long 751s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '72' because it was < 2 characters long 751s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 751s Warning: skipping read '77' because it was < 2 characters long 751s 93 reads; of these: 751s 93 (100.00%) were unpaired; of these: 751s 93 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s Read 50 alignments... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s /usr/bin/bowtie2 --np 6 --norc -M 3 --cp-min 4 --gbar 8 --rfg 27.4582023988232 --score-min L,7.18656816466632,8.3949211978206 --mm --local --cp-ival 4 -N 0 -L26 --trim3 3 -r -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s Processing line... 751s --- Summary --- 751s Read 1 reference strings 751s Checked 0 alignments, 0 edits 751s --------------- 751s PASSED 751s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 751s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 751s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '2' because it was < 2 characters long 751s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '8' because it was < 2 characters long 751s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '23' because it was < 2 characters long 751s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '25' because it was < 2 characters long 751s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '27' because it was < 2 characters long 751s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '31' because it was < 2 characters long 751s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '38' because it was < 2 characters long 751s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '46' because it was < 2 characters long 751s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '47' because it was < 2 characters long 751s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '55' because it was < 2 characters long 751s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '64' because it was < 2 characters long 751s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '67' because it was < 2 characters long 751s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 751s Warning: skipping read '72' because it was < 2 characters long 751s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 751s Warning: skipping read '77' because it was < 2 characters long 751s 93 reads; of these: 751s 93 (100.00%) were unpaired; of these: 751s 93 (100.00%) aligned 0 times 751s 0 (0.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 0.00% overall alignment rate 751s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 751s Flattened IUPAC characters 751s Mutating sequence Sim.pm.1 751s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutating sequence Sim.pm.2 751s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 751s Finished SNPs 751s Finished ref gaps 751s Finished read gaps 751s Mutated reference genome to subject genome 751s SNPs introduced: 6 751s Reference gaps introduced: 0 751s Read gaps introduced: 2 751s Rearrangements introduced: 1 751s Created read sampler 751s Sampling 48 reads 751s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 751s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 751s parsing sequence Sim.pm.1... 751s parsing sequence Sim.pm.2... 751s Parsed 58 reference bases 751s *** Run 3 of 100 752s /usr/bin/bowtie2 --ma 36.0133555802215 --cp-min 11 --cp-ival 1 --trim5 4 -k 4 --score-min L,7.04859686974936,2.85262978937176 --rfg 36.2212235684525 --rdg 5.20228466819702 --np 1 --gbar 3 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 752s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 752s 48 reads; of these: 752s 43 (89.58%) were paired; of these: 752s 43 (100.00%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 0 (0.00%) aligned concordantly >1 times 752s ---- 752s 43 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 43 pairs aligned 0 times concordantly or discordantly; of these: 752s 86 mates make up the pairs; of these: 752s 81 (94.19%) aligned 0 times 752s 4 (4.65%) aligned exactly 1 time 752s 1 (1.16%) aligned >1 times 752s 5 (10.42%) were unpaired; of these: 752s 4 (80.00%) aligned 0 times 752s 1 (20.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 6.59% overall alignment rate 752s Read 50 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CAACGCG 752s CAACGCG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CT 752s CT 752s Processing line... 752s CT 752s CT 752s Processing line... 752s CT 752s CT 752s Processing line... 752s CT 752s CT 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CTTACAACAACGCG 752s CTTACAACAACGCG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCCTTACAACAACGCG 752s GCCTTACAACAACGCG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TTAC 752s TTAC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CACTG 752s CACTG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 9 alignments, 0 edits 752s --------------- 752s PASSED 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.2 752s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.1 752s Introducing 9 SNPs, 1/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 18 752s Reference gaps introduced: 1 752s Read gaps introduced: 0 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 29 reads 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s *** Run 4 of 100 752s /usr/bin/bowtie2 --nofw --cp-min 6 --cp-ival 2 --mm --score-min L,3.47014778385058,8.09293746291645 --rfg 21.2783120617534 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 752s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 752s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '13' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 752s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '14' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 752s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '16' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 752s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '17' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 752s 29 reads; of these: 752s 29 (100.00%) were unpaired; of these: 752s 23 (79.31%) aligned 0 times 752s 2 (6.90%) aligned exactly 1 time 752s 4 (13.79%) aligned >1 times 752s 20.69% overall alignment rate 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CAAC 752s CAAC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AAC 752s AAC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AC 752s AC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CTAG 752s CTAG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GC 752s GC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CACTGCT 752s CACTGCT 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 6 alignments, 0 edits 752s --------------- 752s PASSED 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.2 752s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.1 752s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 4 752s Reference gaps introduced: 0 752s Read gaps introduced: 1 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 78 reads 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s *** Run 5 of 100 752s /usr/bin/bowtie2 -i L,0.282349071232449 --trim5 8 --cp-min 3 --score-min L,3.40346526135437,9.77202720736261 --rfg 45.1424254328507,2.12813832838636 --gbar 2 --mm -a --mp 4.48435875315708,4.06066289784217 -N 0 -L16 --local --cp-ival 2 --trim3 5 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 752s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '1' because it was < 2 characters long 752s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '2' because it was < 2 characters long 752s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '4' because it was < 2 characters long 752s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '9' because it was < 2 characters long 752s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '10' because it was < 2 characters long 752s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '14' because it was < 2 characters long 752s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '15' because it was < 2 characters long 752s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '16' because it was < 2 characters long 752s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '17' because it was < 2 characters long 752s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '19' because it was < 2 characters long 752s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '21' because it was < 2 characters long 752s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '22' because it was < 2 characters long 752s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '23' because it was < 2 characters long 752s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '25' because it was < 2 characters long 752s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '33' because it was < 2 characters long 752s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '34' because it was < 2 characters long 752s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '35' because it was < 2 characters long 752s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '39' because it was < 2 characters long 752s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '40' because it was < 2 characters long 752s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '41' because it was < 2 characters long 752s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '43' because it was < 2 characters long 752s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '45' because it was < 2 characters long 752s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '47' because it was < 2 characters long 752s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '49' because it was < 2 characters long 752s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '50' because it was < 2 characters long 752s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '51' because it was < 2 characters long 752s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '56' because it was < 2 characters long 752s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '57' because it was < 2 characters long 752s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '59' because it was < 2 characters long 752s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '61' because it was < 2 characters long 752s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '62' because it was < 2 characters long 752s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '65' because it was < 2 characters long 752s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '66' because it was < 2 characters long 752s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '67' because it was < 2 characters long 752s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '69' because it was < 2 characters long 752s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '71' because it was < 2 characters long 752s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '73' because it was < 2 characters long 752s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '75' because it was < 2 characters long 752s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '76' because it was < 2 characters long 752s 78 reads; of these: 752s 78 (100.00%) were unpaired; of these: 752s 78 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Read 50 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 0 alignments, 0 edits 752s --------------- 752s PASSED 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 2 752s Reference gaps introduced: 0 752s Read gaps introduced: 0 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 80 reads 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s *** Run 6 of 100 752s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --nofw -R 2 --score-min L,9.44351386357969,9.10014706175425 --rfg 6.75905549317585,17.9060267703665 --rdg 36.2765811004254 --norc --mm -a -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 752s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 752s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '8' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 752s 80 reads; of these: 752s 80 (100.00%) were unpaired; of these: 752s 80 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Read 50 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 0 alignments, 0 edits 752s --------------- 752s PASSED 752s ALSO checking that bowtie2 and bowtie2-align match up 752s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --nofw -R 2 --score-min L,9.44351386357969,9.10014706175425 --rfg 6.75905549317585,17.9060267703665 --rdg 36.2765811004254 --norc --mm -a -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 752s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 752s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '8' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 752s 80 reads; of these: 752s 80 (100.00%) were unpaired; of these: 752s 80 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 752s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 752s /usr/bin/bowtie2 --cp-min 3 --cp-ival 1 --nofw -R 2 --score-min L,9.44351386357969,9.10014706175425 --rfg 6.75905549317585,17.9060267703665 --rdg 36.2765811004254 --norc --mm -a -r -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 752s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 752s *** Run 7 of 100 752s /usr/bin/bowtie2 --cp-min 7 --np 13 --norc --trim3 1 --local --cp-ival 2 --n-ceil 0.866527812860377,1.08603999242811 --mp 5.12261873596469,2.31716261709054 -N 1 -L16 --mm --score-min L,1.4422655266675,3.96483023977399 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 752s /usr/bin/bowtie2 --cp-min 7 --np 13 --norc --trim3 1 --local --cp-ival 2 --n-ceil 0.866527812860377,1.08603999242811 --mp 5.12261873596469,2.31716261709054 -N 1 -L16 --mm --score-min L,1.4422655266675,3.96483023977399 -r -p 3 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 752s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 752s /usr/bin/bowtie2 --cp-min 7 --np 13 --norc --trim3 1 --local --cp-ival 2 --n-ceil 0.866527812860377,1.08603999242811 --mp 5.12261873596469,2.31716261709054 -N 1 -L16 --mm --score-min L,1.4422655266675,3.96483023977399 -r -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 752s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 752s *** Run 8 of 100 752s /usr/bin/bowtie2 -R 3 --cp-min 5 --trim5 8 --trim3 7 -D 4 --cp-ival 1 --mp 8.37412371709967,5.73617566915924 -a --rfg 44.3181980760055,6.66077425152334 --rdg 11.1282877590994,19.5824513973242 --score-min L,6.65819781177995,4.32607932561857 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 752s *** Run 9 of 100 752s /usr/bin/bowtie2 --rdg 44.9987990017505 --score-min L,5.64675875891675,1.74397395376013 --gbar 2 --mp 6.66061985499817,5.23138055562384 --cp-ival 1 --n-ceil 1.49875937141224,0.628252024250767 --np 4 -M 2 -i L,1.388623545893 --cp-min 9 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 752s /usr/bin/bowtie2 --rdg 44.9987990017505 --score-min L,5.64675875891675,1.74397395376013 --gbar 2 --mp 6.66061985499817,5.23138055562384 --cp-ival 1 --n-ceil 1.49875937141224,0.628252024250767 --np 4 -M 2 -i L,1.388623545893 --cp-min 9 --qseq -p 4 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 752s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 752s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 752s Warning: skipping read '8' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 752s 80 reads; of these: 752s 80 (100.00%) were unpaired; of these: 752s 80 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.2 752s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.1 752s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 3 752s Reference gaps introduced: 1 752s Read gaps introduced: 0 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 34 reads 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 752s Warning: skipping read '9' because it was < 2 characters long 752s Warning: skipping read '19' because length (1) <= # seed mismatches (1) 752s Warning: skipping read '19' because it was < 2 characters long 752s 34 reads; of these: 752s 34 (100.00%) were unpaired; of these: 752s 34 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 0 alignments, 0 edits 752s --------------- 752s PASSED 752s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 752s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 752s Warning: skipping read '9' because it was < 2 characters long 752s Warning: skipping read '19' because length (1) <= # seed mismatches (1) 752s Warning: skipping read '19' because it was < 2 characters long 752s 34 reads; of these: 752s 34 (100.00%) were unpaired; of these: 752s 34 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 752s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 752s Warning: skipping read '9' because it was < 2 characters long 752s Warning: skipping read '19' because length (1) <= # seed mismatches (1) 752s Warning: skipping read '19' because it was < 2 characters long 752s 34 reads; of these: 752s 34 (100.00%) were unpaired; of these: 752s 34 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.2 752s Introducing 13 SNPs, 0/1 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.1 752s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 17 752s Reference gaps introduced: 0 752s Read gaps introduced: 1 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 67 reads 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 752s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '0' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 752s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '3' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 752s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '4' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 752s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '5' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 752s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '7' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 752s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '8' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 752s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '16' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 752s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '19' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 752s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '23' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 752s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '24' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 752s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '25' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 752s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '26' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 752s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '27' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 752s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '32' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 752s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '37' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 752s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '38' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 752s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '40' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 752s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '41' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 752s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '47' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 752s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '52' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 752s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '60' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 752s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '63' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 752s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '66' because it was < 2 characters long 752s 67 reads; of these: 752s 53 (79.10%) were paired; of these: 752s 53 (100.00%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 0 (0.00%) aligned concordantly >1 times 752s ---- 752s 53 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 53 pairs aligned 0 times concordantly or discordantly; of these: 752s 106 mates make up the pairs; of these: 752s 101 (95.28%) aligned 0 times 752s 2 (1.89%) aligned exactly 1 time 752s 3 (2.83%) aligned >1 times 752s 14 (20.90%) were unpaired; of these: 752s 14 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 4.17% overall alignment rate 752s Read 50 alignments... 752s Read 100 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCC 752s GCC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCTCTCCTATAG 752s GCTCTCCTATAG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CGC 752s CGC 752s Processing line... 752s GCG 752s GCG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CTAT 752s CTAT 752s Processing line... 752s ATAG 752s ATAG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s ACT 752s ACT 752s Processing line... 752s ACT 752s ACT 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 8 alignments, 0 edits 752s --------------- 752s PASSED 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 15 752s Reference gaps introduced: 0 752s Read gaps introduced: 0 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 57 reads 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 752s Warning: skipping mate #2 of read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 752s 57 reads; of these: 752s 57 (100.00%) were paired; of these: 752s 56 (98.25%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 1 (1.75%) aligned concordantly >1 times 752s ---- 752s 56 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 56 pairs aligned 0 times concordantly or discordantly; of these: 752s 112 mates make up the pairs; of these: 752s 104 (92.86%) aligned 0 times 752s 3 (2.68%) aligned exactly 1 time 752s 5 (4.46%) aligned >1 times 752s 8.77% overall alignment rate 752s Read 50 alignments... 752s Read 100 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AA 752s AA 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCG 752s GCG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AGC 752s AGC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s ATC 752s ATC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AC 752s AC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TA 752s TA 752s Processing line... 752s TCT 752s TCT 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TCT 752s TCT 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCCT 752s GCCT 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AAA 752s AAA 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 10 alignments, 0 edits 752s --------------- 752s PASSED 752s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 752s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 752s Warning: skipping mate #2 of read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 752s 57 reads; of these: 752s 57 (100.00%) were paired; of these: 752s 56 (98.25%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 1 (1.75%) aligned concordantly >1 times 752s ---- 752s 56 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 56 pairs aligned 0 times concordantly or discordantly; of these: 752s 112 mates make up the pairs; of these: 752s 104 (92.86%) aligned 0 times 752s 3 (2.68%) aligned exactly 1 time 752s 5 (4.46%) aligned >1 times 752s 8.77% overall alignment rate 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 752s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 752s *** Run 10 of 100 752s /usr/bin/bowtie2 --trim5 1 --rdg 10.9358620883656 --score-min L,7.52621298643207,8.25176126994179 --np 4 --nofw --cp-ival 1 --cp-min 2 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 3 752s Reference gaps introduced: 2 752s Read gaps introduced: 0 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 29 reads 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s 29 reads; of these: 752s 29 (100.00%) were unpaired; of these: 752s 26 (89.66%) aligned 0 times 752s 3 (10.34%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 10.34% overall alignment rate 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s ACTG 752s ACTG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCTCTCC 752s GCTCTCC 752s Processing line... 752s Processing line... 752s Processing line... 752s CTG 752s CTG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 3 alignments, 0 edits 752s --------------- 752s PASSED 752s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 752s /usr/bin/bowtie2 --trim5 1 --rdg 10.9358620883656 --score-min L,7.52621298643207,8.25176126994179 --np 4 --nofw --cp-ival 1 --cp-min 2 --qseq -p 2 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s 29 reads; of these: 752s 29 (100.00%) were unpaired; of these: 752s 26 (89.66%) aligned 0 times 752s 3 (10.34%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 10.34% overall alignment rate 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 752s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 2 752s Reference gaps introduced: 1 752s Read gaps introduced: 0 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 129 reads 752s *** Run 11 of 100 752s /usr/bin/bowtie2 --score-min L,4.32077222702356,9.11621330998751 -a --mm --mp 4.5622483248781,3.87992745814558 --ma 29.3505562785069 --cp-ival 1 --cp-min 8 --trim3 9 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 752s Read 50 alignments... 752s Read 100 alignments... 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 752s Read 150 alignments... 752s 129 reads; of these: 752s 110 (85.27%) were paired; of these: 752s 110 (100.00%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 0 (0.00%) aligned concordantly >1 times 752s ---- 752s 110 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 110 pairs aligned 0 times concordantly or discordantly; of these: 752s 220 mates make up the pairs; of these: 752s 207 (94.09%) aligned 0 times 752s 5 (2.27%) aligned exactly 1 time 752s 8 (3.64%) aligned >1 times 752s 19 (14.73%) were unpaired; of these: 752s 17 (89.47%) aligned 0 times 752s 2 (10.53%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 6.28% overall alignment rate 752s Read 200 alignments... 752s Read 250 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s CAC 752s CAC 752s Processing line... 752s CAC 752s CAC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCA 752s GCA 752s Processing line... 752s TGC 752s TGC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s ACAACGC 752s ACAACGC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AA 752s AA 752s Processing line... 752s TT 752s TT 752s Processing line... 752s AA 752s AA 752s Processing line... 752s AA 752s AA 752s Processing line... 752s AA 752s AA 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s ACA 752s ACA 752s Processing line... 752s ACA 752s ACA 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s ACTG 752s ACTG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TACAACAACG 752s TACAACAACG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s GCCTTACA 752s GCCTTACA 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s AA 752s AA 752s Processing line... 752s AA 752s AA 752s Processing line... 752s TT 752s TT 752s Processing line... 752s AA 752s AA 752s Processing line... 752s AA 752s AA 752s Processing line... 752s Processing line... 752s ACAACAACG 752s ACAACAACG 752s Processing line... 752s Processing line... 752s CACT 752s CACT 752s Processing line... 752s CACT 752s CACT 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s ACAACAACG 752s ACAACAACG 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TA 752s TA 752s Processing line... 752s TA 752s TA 752s Processing line... 752s TA 752s TA 752s Processing line... 752s TA 752s TA 752s Processing line... 752s TA 752s TA 752s Processing line... 752s TA 752s TA 752s Processing line... 752s /usr/bin/bowtie2 --score-min L,4.32077222702356,9.11621330998751 -a --mm --mp 4.5622483248781,3.87992745814558 --ma 29.3505562785069 --cp-ival 1 --cp-min 8 --trim3 9 --qseq -p 3 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 752s TA 752s TA 752s Processing line... 752s TA 752s TA 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s TAG 752s TAG 752s Processing line... 752s CTA 752s CTA 752s Processing line... 752s CTA 752s CTA 752s Processing line... 752s TAG 752s TAG 752s Processing line... 752s Processing line... 752s CTTACAACAACGC 752s CTTACAACAACGC 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 37 alignments, 0 edits 752s --------------- 752s PASSED 752s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 752s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 752s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 752s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 752s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 752s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 752s 129 reads; of these: 752s 110 (85.27%) were paired; of these: 752s 110 (100.00%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 0 (0.00%) aligned concordantly >1 times 752s ---- 752s 110 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 110 pairs aligned 0 times concordantly or discordantly; of these: 752s 220 mates make up the pairs; of these: 752s 207 (94.09%) aligned 0 times 752s 5 (2.27%) aligned exactly 1 time 752s 8 (3.64%) aligned >1 times 752s 19 (14.73%) were unpaired; of these: 752s 17 (89.47%) aligned 0 times 752s 2 (10.53%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 6.28% overall alignment rate 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 752s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 752s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 752s Flattened IUPAC characters 752s Mutating sequence Sim.pm.1 752s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutating sequence Sim.pm.2 752s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 752s Finished SNPs 752s Finished ref gaps 752s Finished read gaps 752s Mutated reference genome to subject genome 752s SNPs introduced: 4 752s Reference gaps introduced: 0 752s Read gaps introduced: 0 752s Rearrangements introduced: 0 752s Created read sampler 752s Sampling 26 reads 752s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 752s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 752s parsing sequence Sim.pm.1... 752s parsing sequence Sim.pm.2... 752s Parsed 58 reference bases 752s *** Run 12 of 100 752s /usr/bin/bowtie2 -R 2 --cp-min 7 -i L,0.201912941952515 --trim5 6 --nofw -N 0 -L16 --mp 8.16616059007293,7.52334538636932 --cp-ival 3 --local --mm --score-min L,6.35288209421326,2.42391244463276 --gbar 3 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 752s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '3' because it was < 2 characters long 752s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '5' because it was < 2 characters long 752s Warning: skipping mate #2 of read '5' because it was < 2 characters long 752s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '14' because it was < 2 characters long 752s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '20' because it was < 2 characters long 752s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '22' because it was < 2 characters long 752s 26 reads; of these: 752s 20 (76.92%) were paired; of these: 752s 20 (100.00%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 0 (0.00%) aligned concordantly >1 times 752s ---- 752s 20 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 20 pairs aligned 0 times concordantly or discordantly; of these: 752s 40 mates make up the pairs; of these: 752s 40 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 6 (23.08%) were unpaired; of these: 752s 6 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s Read 50 alignments... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s Processing line... 752s --- Summary --- 752s Read 1 reference strings 752s Checked 0 alignments, 0 edits 752s --------------- 752s PASSED 752s ALSO checking that bowtie2 and bowtie2-align match up 752s /usr/bin/bowtie2 -R 2 --cp-min 7 -i L,0.201912941952515 --trim5 6 --nofw -N 0 -L16 --mp 8.16616059007293,7.52334538636932 --cp-ival 3 --local --mm --score-min L,6.35288209421326,2.42391244463276 --gbar 3 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 752s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '3' because it was < 2 characters long 752s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '5' because it was < 2 characters long 752s Warning: skipping mate #2 of read '5' because it was < 2 characters long 752s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '14' because it was < 2 characters long 752s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 752s Warning: skipping read '20' because it was < 2 characters long 752s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 752s Warning: skipping mate #1 of read '22' because it was < 2 characters long 752s 26 reads; of these: 752s 20 (76.92%) were paired; of these: 752s 20 (100.00%) aligned concordantly 0 times 752s 0 (0.00%) aligned concordantly exactly 1 time 752s 0 (0.00%) aligned concordantly >1 times 752s ---- 752s 20 pairs aligned concordantly 0 times; of these: 752s 0 (0.00%) aligned discordantly 1 time 752s ---- 752s 20 pairs aligned 0 times concordantly or discordantly; of these: 752s 40 mates make up the pairs; of these: 752s 40 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 6 (23.08%) were unpaired; of these: 752s 6 (100.00%) aligned 0 times 752s 0 (0.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 0.00% overall alignment rate 752s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 752s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 752s /usr/bin/bowtie2 -R 2 --cp-min 7 -i L,0.201912941952515 --trim5 6 --nofw -N 0 -L16 --mp 8.16616059007293,7.52334538636932 --cp-ival 3 --local --mm --score-min L,6.35288209421326,2.42391244463276 --gbar 3 -r -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '3' because it was < 2 characters long 753s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '5' because it was < 2 characters long 753s Warning: skipping mate #2 of read '5' because it was < 2 characters long 753s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '14' because it was < 2 characters long 753s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '20' because it was < 2 characters long 753s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '22' because it was < 2 characters long 753s 26 reads; of these: 753s 20 (76.92%) were paired; of these: 753s 20 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 20 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 20 pairs aligned 0 times concordantly or discordantly; of these: 753s 40 mates make up the pairs; of these: 753s 40 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 6 (23.08%) were unpaired; of these: 753s 6 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s Flattened IUPAC characters 753s Mutating sequence Sim.pm.2 753s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutating sequence Sim.pm.1 753s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutated reference genome to subject genome 753s SNPs introduced: 5 753s Reference gaps introduced: 1 753s Read gaps introduced: 0 753s Rearrangements introduced: 1 753s Created read sampler 753s Sampling 12 reads 753s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 753s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 753s parsing sequence Sim.pm.1... 753s parsing sequence Sim.pm.2... 753s Parsed 58 reference bases 753s *** Run 13 of 100 753s /usr/bin/bowtie2 --mm --score-min L,3.85601681692592,7.95460517198846 --rfg 15.7626240331787,14.7749994587502 --nofw --mp 6.82080965245553,2.77629692991508 --cp-ival 1 --local -M 8 --trim5 9 --cp-min 2 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '0' because it was < 2 characters long 753s /usr/bin/bowtie2 --mm --score-min L,3.85601681692592,7.95460517198846 --rfg 15.7626240331787,14.7749994587502 --nofw --mp 6.82080965245553,2.77629692991508 --cp-ival 1 --local -M 8 --trim5 9 --cp-min 2 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 753s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 753s /usr/bin/bowtie2 --mm --score-min L,3.85601681692592,7.95460517198846 --rfg 15.7626240331787,14.7749994587502 --nofw --mp 6.82080965245553,2.77629692991508 --cp-ival 1 --local -M 8 --trim5 9 --cp-min 2 -r -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s 12 reads; of these: 753s 8 (66.67%) were paired; of these: 753s 8 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 8 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 8 pairs aligned 0 times concordantly or discordantly; of these: 753s 16 mates make up the pairs; of these: 753s 16 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 4 (33.33%) were unpaired; of these: 753s 4 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 0 alignments, 0 edits 753s --------------- 753s PASSED 753s ALSO checking that bowtie2 and bowtie2-align match up 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '0' because it was < 2 characters long 753s 12 reads; of these: 753s 8 (66.67%) were paired; of these: 753s 8 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 8 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 8 pairs aligned 0 times concordantly or discordantly; of these: 753s 16 mates make up the pairs; of these: 753s 16 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 4 (33.33%) were unpaired; of these: 753s 4 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read '0' because it was < 2 characters long 753s 12 reads; of these: 753s 8 (66.67%) were paired; of these: 753s 8 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 8 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 8 pairs aligned 0 times concordantly or discordantly; of these: 753s 16 mates make up the pairs; of these: 753s 16 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 4 (33.33%) were unpaired; of these: 753s 4 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s Flattened IUPAC characters 753s Mutating sequence Sim.pm.1 753s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutating sequence Sim.pm.2 753s Introducing 3 SNPs, 0/1 ref/read gaps, and 1 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutated reference genome to subject genome 753s SNPs introduced: 5 753s Reference gaps introduced: 0 753s Read gaps introduced: 1 753s Rearrangements introduced: 1 753s Created read sampler 753s Sampling 156 reads 753s *** Run 14 of 100 753s /usr/bin/bowtie2 -M 2 --trim5 6 --np 5 --cp-min 3 --rfg 8.3944942241218 --score-min L,3.54548909765043,5.17210408608841 --gbar 6 --local --cp-ival 2 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 753s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 753s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 753s parsing sequence Sim.pm.1... 753s parsing sequence Sim.pm.2... 753s Parsed 58 reference bases 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '4' because it was < 2 characters long 753s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '5' because it was < 2 characters long 753s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '11' because it was < 2 characters long 753s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '16' because it was < 2 characters long 753s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '23' because it was < 2 characters long 753s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '28' because it was < 2 characters long 753s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '34' because it was < 2 characters long 753s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '36' because it was < 2 characters long 753s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '39' because it was < 2 characters long 753s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '43' because it was < 2 characters long 753s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 753s Warning: skipping read '49' because it was < 2 characters long 753s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '55' because it was < 2 characters long 753s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '57' because it was < 2 characters long 753s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '64' because it was < 2 characters long 753s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '66' because it was < 2 characters long 753s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '67' because it was < 2 characters long 753s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '73' because it was < 2 characters long 753s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '74' because it was < 2 characters long 753s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '84' because it was < 2 characters long 753s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '90' because it was < 2 characters long 753s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '93' because it was < 2 characters long 753s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '94' because it was < 2 characters long 753s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '101' because it was < 2 characters long 753s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '103' because it was < 2 characters long 753s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '106' because it was < 2 characters long 753s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '108' because it was < 2 characters long 753s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '112' because it was < 2 characters long 753s Warning: skipping read '114' because length (1) <= # seed mismatches (0) 753s Warning: skipping read '114' because it was < 2 characters long 753s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '120' because it was < 2 characters long 753s Warning: skipping read '128' because length (1) <= # seed mismatches (0) 753s Warning: skipping read '128' because it was < 2 characters long 753s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '129' because it was < 2 characters long 753s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '132' because it was < 2 characters long 753s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '134' because it was < 2 characters long 753s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '135' because it was < 2 characters long 753s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '136' because it was < 2 characters long 753s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '143' because it was < 2 characters long 753s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '144' because it was < 2 characters long 753s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '147' because it was < 2 characters long 753s Warning: skipping read '149' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '149' because it was < 2 characters long 753s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '152' because it was < 2 characters long 753s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '154' because it was < 2 characters long 753s 156 reads; of these: 753s 156 (100.00%) were unpaired; of these: 753s 156 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s Read 50 alignments... 753s Read 100 alignments... 753s Read 150 alignments... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 0 alignments, 0 edits 753s --------------- 753s PASSED 753s ALSO checking that bowtie2 and bowtie2-align match up 753s /usr/bin/bowtie2 -M 2 --trim5 6 --np 5 --cp-min 3 --rfg 8.3944942241218 --score-min L,3.54548909765043,5.17210408608841 --gbar 6 --local --cp-ival 2 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 753s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 753s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '4' because it was < 2 characters long 753s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '5' because it was < 2 characters long 753s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '11' because it was < 2 characters long 753s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '16' because it was < 2 characters long 753s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '23' because it was < 2 characters long 753s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '28' because it was < 2 characters long 753s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '34' because it was < 2 characters long 753s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '36' because it was < 2 characters long 753s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '39' because it was < 2 characters long 753s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '43' because it was < 2 characters long 753s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 753s Warning: skipping read '49' because it was < 2 characters long 753s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '55' because it was < 2 characters long 753s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '57' because it was < 2 characters long 753s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '64' because it was < 2 characters long 753s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '66' because it was < 2 characters long 753s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '67' because it was < 2 characters long 753s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '73' because it was < 2 characters long 753s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '74' because it was < 2 characters long 753s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '84' because it was < 2 characters long 753s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '90' because it was < 2 characters long 753s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '93' because it was < 2 characters long 753s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '94' because it was < 2 characters long 753s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '101' because it was < 2 characters long 753s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '103' because it was < 2 characters long 753s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '106' because it was < 2 characters long 753s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '108' because it was < 2 characters long 753s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '112' because it was < 2 characters long 753s Warning: skipping read '114' because length (1) <= # seed mismatches (0) 753s Warning: skipping read '114' because it was < 2 characters long 753s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '120' because it was < 2 characters long 753s Warning: skipping read '128' because length (1) <= # seed mismatches (0) 753s Warning: skipping read '128' because it was < 2 characters long 753s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '129' because it was < 2 characters long 753s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '132' because it was < 2 characters long 753s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '134' because it was < 2 characters long 753s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '135' because it was < 2 characters long 753s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '136' because it was < 2 characters long 753s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '143' because it was < 2 characters long 753s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '144' because it was < 2 characters long 753s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '147' because it was < 2 characters long 753s Warning: skipping read '149' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '149' because it was < 2 characters long 753s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '152' because it was < 2 characters long 753s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 753s Warning: skipping read '154' because it was < 2 characters long 753s 156 reads; of these: 753s 156 (100.00%) were unpaired; of these: 753s 156 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 753s Flattened IUPAC characters 753s Mutating sequence Sim.pm.1 753s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutating sequence Sim.pm.2 753s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutated reference genome to subject genome 753s SNPs introduced: 7 753s Reference gaps introduced: 0 753s Read gaps introduced: 0 753s Rearrangements introduced: 3 753s Created read sampler 753s Sampling 92 reads 753s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 753s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 753s parsing sequence Sim.pm.1... 753s parsing sequence Sim.pm.2... 753s Parsed 58 reference bases 753s *** Run 15 of 100 753s /usr/bin/bowtie2 -N 1 -L22 --mp 5.16050586599996,4.85101690764373 --nofw --cp-ival 2 --n-ceil 1.05736085138082,0.047663305910016 --rdg 27.9081501738135,9.5061562256996 --score-min L,1.60282193601125,4.60878456511846 -a --ma 30.7020208284593 --cp-min 4 --norc -i L,0.103738411710488 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 753s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 753s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 753s 92 reads; of these: 753s 92 (100.00%) were unpaired; of these: 753s 92 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s Read 50 alignments... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s /usr/bin/bowtie2 -N 1 -L22 --mp 5.16050586599996,4.85101690764373 --nofw --cp-ival 2 --n-ceil 1.05736085138082,0.047663305910016 --rdg 27.9081501738135,9.5061562256996 --score-min L,1.60282193601125,4.60878456511846 -a --ma 30.7020208284593 --cp-min 4 --norc -i L,0.103738411710488 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 0 alignments, 0 edits 753s --------------- 753s PASSED 753s ALSO checking that bowtie2 and bowtie2-align match up 753s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 753s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 753s 92 reads; of these: 753s 92 (100.00%) were unpaired; of these: 753s 92 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 753s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 753s /usr/bin/bowtie2 -N 1 -L22 --mp 5.16050586599996,4.85101690764373 --nofw --cp-ival 2 --n-ceil 1.05736085138082,0.047663305910016 --rdg 27.9081501738135,9.5061562256996 --score-min L,1.60282193601125,4.60878456511846 -a --ma 30.7020208284593 --cp-min 4 --norc -i L,0.103738411710488 -q -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 753s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 753s 92 reads; of these: 753s 92 (100.00%) were unpaired; of these: 753s 92 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s Flattened IUPAC characters 753s Mutating sequence Sim.pm.1 753s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutating sequence Sim.pm.2 753s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutated reference genome to subject genome 753s SNPs introduced: 6 753s Reference gaps introduced: 1 753s Read gaps introduced: 1 753s Rearrangements introduced: 0 753s Created read sampler 753s Sampling 51 reads 753s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 753s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 753s parsing sequence Sim.pm.1... 753s parsing sequence Sim.pm.2... 753s Parsed 58 reference bases 753s *** Run 16 of 100 753s /usr/bin/bowtie2 --score-min L,4.12221486977686,6.58450719233747 --rfg 47.7724092945712,4.96590862753905 -k 2 --cp-min 6 --cp-ival 1 --local --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 753s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 753s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 753s 51 reads; of these: 753s 51 (100.00%) were unpaired; of these: 753s 51 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s Read 50 alignments... 753s /usr/bin/bowtie2 --score-min L,4.12221486977686,6.58450719233747 --rfg 47.7724092945712,4.96590862753905 -k 2 --cp-min 6 --cp-ival 1 --local --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 0 alignments, 0 edits 753s --------------- 753s PASSED 753s ALSO checking that bowtie2 and bowtie2-align match up 753s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 753s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 753s 51 reads; of these: 753s 51 (100.00%) were unpaired; of these: 753s 51 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 753s /usr/bin/bowtie2 --score-min L,4.12221486977686,6.58450719233747 --rfg 47.7724092945712,4.96590862753905 -k 2 --cp-min 6 --cp-ival 1 --local --qseq -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 753s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 753s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 753s 51 reads; of these: 753s 51 (100.00%) were unpaired; of these: 753s 51 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s Flattened IUPAC characters 753s Mutating sequence Sim.pm.2 753s Introducing 1 SNPs, 1/2 ref/read gaps, and 0 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutating sequence Sim.pm.1 753s Introducing 3 SNPs, 2/0 ref/read gaps, and 0 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutated reference genome to subject genome 753s SNPs introduced: 4 753s Reference gaps introduced: 3 753s Read gaps introduced: 2 753s Rearrangements introduced: 0 753s Created read sampler 753s Sampling 89 reads 753s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 753s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 753s parsing sequence Sim.pm.1... 753s parsing sequence Sim.pm.2... 753s Parsed 58 reference bases 753s *** Run 17 of 100 753s /usr/bin/bowtie2 --score-min L,9.29169485941253,2.30171683926412 --trim5 8 --mp 6.30091886063018,2.32654690824286 --cp-ival 1 --local --cp-min 3 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 753s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 753s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 753s Read 50 alignments... 753s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 753s Read 100 alignments... 753s 89 reads; of these: 753s 76 (85.39%) were paired; of these: 753s 76 (100.00%) aligned concordantly 0 times 753s 0 (0.00%) aligned concordantly exactly 1 time 753s 0 (0.00%) aligned concordantly >1 times 753s ---- 753s 76 pairs aligned concordantly 0 times; of these: 753s 0 (0.00%) aligned discordantly 1 time 753s ---- 753s 76 pairs aligned 0 times concordantly or discordantly; of these: 753s 152 mates make up the pairs; of these: 753s 152 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 13 (14.61%) were unpaired; of these: 753s 13 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s Read 150 alignments... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 0 alignments, 0 edits 753s --------------- 753s PASSED 753s Flattened IUPAC characters 753s Mutating sequence Sim.pm.1 753s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutating sequence Sim.pm.2 753s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 753s Finished SNPs 753s Finished ref gaps 753s Finished read gaps 753s Mutated reference genome to subject genome 753s SNPs introduced: 7 753s Reference gaps introduced: 0 753s Read gaps introduced: 0 753s Rearrangements introduced: 1 753s Created read sampler 753s Sampling 16 reads 753s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 753s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 753s parsing sequence Sim.pm.1... 753s parsing sequence Sim.pm.2... 753s Parsed 58 reference bases 753s *** Run 18 of 100 753s /usr/bin/bowtie2 --score-min L,1.67335644189049,5.4524202022961 --rdg 7.36906674102446,6.91094123452437 --rfg 42.558900064559,16.3881273330147 --trim5 7 --ma 27.8487595162096 --mp 6.09935214437774,3.14108672039228 --cp-min 3 --cp-ival 1 -R 1 --trim3 3 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 753s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 753s 16 reads; of these: 753s 16 (100.00%) were unpaired; of these: 753s 16 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s Processing line... 753s --- Summary --- 753s Read 1 reference strings 753s Checked 0 alignments, 0 edits 753s --------------- 753s PASSED 753s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 753s /usr/bin/bowtie2 --score-min L,1.67335644189049,5.4524202022961 --rdg 7.36906674102446,6.91094123452437 --rfg 42.558900064559,16.3881273330147 --trim5 7 --ma 27.8487595162096 --mp 6.09935214437774,3.14108672039228 --cp-min 3 --cp-ival 1 -R 1 --trim3 3 --qseq -p 2 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 753s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 753s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 753s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 753s 16 reads; of these: 753s 16 (100.00%) were unpaired; of these: 753s 16 (100.00%) aligned 0 times 753s 0 (0.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 0.00% overall alignment rate 753s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 753s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 753s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 753s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 753s /usr/bin/bowtie2 --score-min L,1.67335644189049,5.4524202022961 --rdg 7.36906674102446,6.91094123452437 --rfg 42.558900064559,16.3881273330147 --trim5 7 --ma 27.8487595162096 --mp 6.09935214437774,3.14108672039228 --cp-min 3 --cp-ival 1 -R 1 --trim3 3 --qseq -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 753s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 753s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 754s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 754s 16 reads; of these: 754s 16 (100.00%) were unpaired; of these: 754s 16 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.1 754s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.2 754s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 13 754s Reference gaps introduced: 1 754s Read gaps introduced: 0 754s Rearrangements introduced: 0 754s Created read sampler 754s Sampling 102 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s *** Run 19 of 100 754s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 1.31975320991083,0.13613197140918 --local --nofw -N 0 -L22 -a --gbar 3 --score-min L,5.88332398751869,9.04397565579877 --rdg 3.13942893401322 --cp-min 6 -i C,4.79348514342971 --trim5 2 --norc -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 754s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '2' because it was < 2 characters long 754s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '4' because it was < 2 characters long 754s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '7' because it was < 2 characters long 754s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '8' because it was < 2 characters long 754s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '14' because it was < 2 characters long 754s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '15' because it was < 2 characters long 754s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '18' because it was < 2 characters long 754s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '27' because it was < 2 characters long 754s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '33' because it was < 2 characters long 754s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '40' because it was < 2 characters long 754s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '42' because it was < 2 characters long 754s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '50' because it was < 2 characters long 754s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '63' because it was < 2 characters long 754s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '64' because it was < 2 characters long 754s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '67' because it was < 2 characters long 754s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '68' because it was < 2 characters long 754s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '75' because it was < 2 characters long 754s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '82' because it was < 2 characters long 754s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '89' because it was < 2 characters long 754s Warning: skipping read '101' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '101' because it was < 2 characters long 754s 102 reads; of these: 754s 102 (100.00%) were unpaired; of these: 754s 102 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s Read 50 alignments... 754s Read 100 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 0 alignments, 0 edits 754s --------------- 754s PASSED 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.1 754s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.2 754s Introducing 7 SNPs, 1/0 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 7 754s Reference gaps introduced: 1 754s Read gaps introduced: 0 754s Rearrangements introduced: 1 754s Created read sampler 754s Sampling 124 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s *** Run 20 of 100 754s /usr/bin/bowtie2 --trim3 4 -R 2 --cp-min 11 --cp-ival 4 --mp 9.01481106563422,4.94170777501779 -k 3 --mm -i S,0.221344423859509 --np 1 --score-min L,4.38859657851547,2.52434495723309 --rfg 18.7923661430139 --rdg 28.7345489032737 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 754s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 754s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '9' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 754s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '11' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 754s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '17' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 754s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '18' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 754s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '23' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 754s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '24' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 754s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '30' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 754s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '36' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 754s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '37' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 754s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '41' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 754s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '42' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 754s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '44' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 754s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '48' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 754s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '63' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 754s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '65' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 754s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '67' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 754s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '87' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 754s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '88' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 754s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '89' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 754s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '91' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 754s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '93' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 754s Warning: skipping read '101' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '101' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 754s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '106' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 754s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '121' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 754s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '122' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 754s 124 reads; of these: 754s 124 (100.00%) were unpaired; of these: 754s 110 (88.71%) aligned 0 times 754s 8 (6.45%) aligned exactly 1 time 754s 6 (4.84%) aligned >1 times 754s 11.29% overall alignment rate 754s Read 50 alignments... 754s Read 100 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CTG 754s CTG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CTCTCCTATAG 754s CTCTCCTATAG 754s Processing line... 754s Processing line... 754s Processing line... 754s ATCT 754s ATCT 754s Processing line... 754s Processing line... 754s Processing line... 754s CAA 754s CAA 754s Processing line... 754s CAA 754s CAA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GCC 754s GCC 754s Processing line... 754s AACAACGC 754s AACAACGC 754s Processing line... 754s Processing line... 754s Processing line... 754s AA 754s AA 754s Processing line... 754s AA 754s AA 754s Processing line... 754s AA 754s AA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TAC 754s TAC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CC 754s CC 754s Processing line... 754s CC 754s CC 754s Processing line... 754s CC 754s CC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s TCTCCTATA 754s TCTCCTATA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CC 754s CC 754s Processing line... 754s CC 754s CC 754s Processing line... 754s CC 754s CC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CG 754s CG 754s Processing line... 754s CG 754s CG 754s Processing line... 754s CG 754s CG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CCCC 754s CCCC 754s --- Summary --- 754s Read 1 reference strings 754s Checked 25 alignments, 0 edits 754s --------------- 754s PASSED 754s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 754s /usr/bin/bowtie2 --trim3 4 -R 2 --cp-min 11 --cp-ival 4 --mp 9.01481106563422,4.94170777501779 -k 3 --mm -i S,0.221344423859509 --np 1 --score-min L,4.38859657851547,2.52434495723309 --rfg 18.7923661430139 --rdg 28.7345489032737 -q -p 4 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 754s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 754s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '9' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 754s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '11' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 754s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '17' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 754s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '18' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 754s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '23' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 754s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '24' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 754s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '30' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 754s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '36' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 754s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '37' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 754s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '41' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 754s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '42' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 754s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '44' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 754s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '48' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 754s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '63' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 754s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '65' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 754s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '67' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 754s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '87' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 754s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '88' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 754s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '89' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 754s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '91' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 754s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '93' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 754s Warning: skipping read '101' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '101' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 754s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '106' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 754s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '121' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 754s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '122' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 754s 124 reads; of these: 754s 124 (100.00%) were unpaired; of these: 754s 110 (88.71%) aligned 0 times 754s 8 (6.45%) aligned exactly 1 time 754s 6 (4.84%) aligned >1 times 754s 11.29% overall alignment rate 754s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.1 754s *** Run 21 of 100 754s /usr/bin/bowtie2 --nofw --ma 21.703220419946 -N 1 -L27 --cp-min 3 --cp-ival 1 --trim3 7 --score-min L,9.56731873155669,4.96730998494725 --norc -a -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 754s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.2 754s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 3 754s Reference gaps introduced: 0 754s Read gaps introduced: 0 754s Rearrangements introduced: 0 754s Created read sampler 754s Sampling 30 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 754s /usr/bin/bowtie2 --nofw --ma 21.703220419946 -N 1 -L27 --cp-min 3 --cp-ival 1 --trim3 7 --score-min L,9.56731873155669,4.96730998494725 --norc -a -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 754s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 754s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '8' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 754s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '11' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 754s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '15' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 754s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '18' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 754s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '23' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 754s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '24' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 754s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '28' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 754s 30 reads; of these: 754s 30 (100.00%) were unpaired; of these: 754s 30 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 0 alignments, 0 edits 754s --------------- 754s PASSED 754s ALSO checking that bowtie2 and bowtie2-align match up 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 754s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 754s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '8' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 754s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '11' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 754s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '15' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 754s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '18' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 754s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '23' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 754s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '24' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 754s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 754s Warning: skipping read '28' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 754s 30 reads; of these: 754s 30 (100.00%) were unpaired; of these: 754s 30 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.1 754s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.2 754s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 5 754s Reference gaps introduced: 1 754s Read gaps introduced: 1 754s Rearrangements introduced: 0 754s Created read sampler 754s Sampling 73 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s *** Run 22 of 100 754s /usr/bin/bowtie2 --trim3 0 -N 0 -L24 --cp-ival 3 -a --rfg 45.359305131501 --rdg 13.1120158166258,14.7270344564682 --score-min L,8.35124159830415,2.06172811018624 --gbar 2 -R 4 --cp-min 9 --trim5 4 -q -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 754s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read '9' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 754s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read '15' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 754s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read '43' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 754s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '56' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 754s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #2 of read '61' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 754s Read 50 alignments... 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 754s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '66' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 754s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '67' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 754s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '69' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 754s Read 100 alignments... 754s 73 reads; of these: 754s 60 (82.19%) were paired; of these: 754s 60 (100.00%) aligned concordantly 0 times 754s 0 (0.00%) aligned concordantly exactly 1 time 754s 0 (0.00%) aligned concordantly >1 times 754s ---- 754s 60 pairs aligned concordantly 0 times; of these: 754s 0 (0.00%) aligned discordantly 1 time 754s ---- 754s 60 pairs aligned 0 times concordantly or discordantly; of these: 754s 120 mates make up the pairs; of these: 754s 111 (92.50%) aligned 0 times 754s 3 (2.50%) aligned exactly 1 time 754s 6 (5.00%) aligned >1 times 754s 13 (17.81%) were unpaired; of these: 754s 13 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 6.77% overall alignment rate 754s Read 150 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CTCT 754s CTCT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AAC 754s AAC 754s Processing line... 754s AAC 754s AAC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TGCT 754s TGCT 754s Processing line... 754s AGCA 754s AGCA 754s Processing line... 754s Processing line... 754s ACAACAA 754s ACAACAA 754s Processing line... 754s Processing line... 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s GC 754s GC 754s Processing line... 754s Processing line... 754s AA 754s AA 754s Processing line... 754s AA 754s AA 754s Processing line... 754s AA 754s AA 754s Processing line... 754s TT 754s TT 754s Processing line... 754s AA 754s AA 754s Processing line... 754s Processing line... 754s AACAA 754s AACAA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AA 754s AA 754s Processing line... 754s AA 754s AA 754s Processing line... 754s AA 754s AA 754s Processing line... 754s AA 754s AA 754s Processing line... 754s TT 754s TT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TG 754s TG 754s Processing line... 754s CA 754s CA 754s Processing line... 754s CA 754s CA 754s Processing line... 754s CA 754s CA 754s Processing line... 754s CA 754s CA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 32 alignments, 0 edits 754s --------------- 754s PASSED 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.2 754s Introducing 1 SNPs, 0/2 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.1 754s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 5 754s Reference gaps introduced: 0 754s Read gaps introduced: 2 754s Rearrangements introduced: 0 754s Created read sampler 754s Sampling 82 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s *** Run 23 of 100 754s /usr/bin/bowtie2 --trim5 8 --np 2 --rdg 14.5159156708293 --score-min L,6.27732553313145,8.76682487324817 --cp-ival 4 --n-ceil 0.586022498929832,0.602085518034766 -D 17 --cp-min 2 --ma 25.0319540303741 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 754s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 754s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '5' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 754s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '6' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 754s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '10' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 754s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '13' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 754s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '15' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 754s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '18' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 754s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '22' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 754s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '23' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 754s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '24' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 754s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '29' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 754s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '32' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 754s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '37' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 754s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '44' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 754s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '51' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 754s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '56' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 754s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '58' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 754s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '62' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 754s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '70' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 754s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '71' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 754s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '79' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 754s 82 reads; of these: 754s 82 (100.00%) were unpaired; of these: 754s 75 (91.46%) aligned 0 times 754s 2 (2.44%) aligned exactly 1 time 754s 5 (6.10%) aligned >1 times 754s 8.54% overall alignment rate 754s Read 50 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CACTGC 754s CACTGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CA 754s CA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AA 754s AA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AA 754s AA 754s Processing line... 754s CA 754s CA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AACAACGC 754s AACAACGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GC 754s GC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 7 alignments, 0 edits 754s --------------- 754s PASSED 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.1 754s Introducing 3 SNPs, 0/2 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.2 754s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 6 754s Reference gaps introduced: 1 754s Read gaps introduced: 2 754s Rearrangements introduced: 1 754s Created read sampler 754s Sampling 156 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s *** Run 24 of 100 754s /usr/bin/bowtie2 --mp 9.03586890923272,8.89184693191526 -N 1 -L13 --ma 19.548043693222 --cp-ival 1 --cp-min 3 --rdg 46.9273541429197,19.6027359083446 --score-min L,4.29052826142633,7.13533822610218 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 754s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #1 of read '17' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 754s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #2 of read '24' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 754s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #2 of read '52' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 754s Read 50 alignments... 754s Read 100 alignments... 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 754s Warning: skipping mate #1 of read '88' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #1 of read '88' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 754s Warning: skipping mate #2 of read '111' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #2 of read '111' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 754s Read 150 alignments... 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 754s Read 200 alignments... 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 754s Warning: skipping mate #1 of read '150' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #1 of read '150' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 754s 156 reads; of these: 754s 156 (100.00%) were paired; of these: 754s 156 (100.00%) aligned concordantly 0 times 754s 0 (0.00%) aligned concordantly exactly 1 time 754s 0 (0.00%) aligned concordantly >1 times 754s ---- 754s 156 pairs aligned concordantly 0 times; of these: 754s 0 (0.00%) aligned discordantly 1 time 754s ---- 754s 156 pairs aligned 0 times concordantly or discordantly; of these: 754s 312 mates make up the pairs; of these: 754s 293 (93.91%) aligned 0 times 754s 8 (2.56%) aligned exactly 1 time 754s 11 (3.53%) aligned >1 times 754s 6.09% overall alignment rate 754s Read 250 alignments... 754s Read 300 alignments... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CT 754s CT 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TGC 754s TGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CC 754s CC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TTACAACAA 754s TTACAACAA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s GCG 754s GCG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CTC 754s CTC 754s Processing line... 754s Processing line... 754s AAA 754s AAA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AA 754s AA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CAACG 754s CAACG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CTTA 754s CTTA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CA 754s CA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s ACAACA 754s ACAACA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TG 754s TG 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TTACAACA 754s TTACAACA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s /usr/bin/bowtie2 --mp 9.03586890923272,8.89184693191526 -N 1 -L13 --ma 19.548043693222 --cp-ival 1 --cp-min 3 --rdg 46.9273541429197,19.6027359083446 --score-min L,4.29052826142633,7.13533822610218 -r -p 3 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AACAACGC 754s AACAACGC 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AACA 754s AACA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s CA 754s CA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s TA 754s TA 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s AA 754s AA 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 19 alignments, 0 edits 754s --------------- 754s PASSED 754s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 754s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #1 of read '17' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 754s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #2 of read '24' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 754s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #2 of read '52' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 754s Warning: skipping mate #1 of read '88' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #1 of read '88' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 754s Warning: skipping mate #2 of read '111' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #2 of read '111' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 754s Warning: skipping mate #1 of read '150' because length (1) <= # seed mismatches (1) 754s Warning: skipping mate #1 of read '150' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 754s 156 reads; of these: 754s 156 (100.00%) were paired; of these: 754s 156 (100.00%) aligned concordantly 0 times 754s 0 (0.00%) aligned concordantly exactly 1 time 754s 0 (0.00%) aligned concordantly >1 times 754s ---- 754s 156 pairs aligned concordantly 0 times; of these: 754s 0 (0.00%) aligned discordantly 1 time 754s ---- 754s 156 pairs aligned 0 times concordantly or discordantly; of these: 754s 312 mates make up the pairs; of these: 754s 293 (93.91%) aligned 0 times 754s 8 (2.56%) aligned exactly 1 time 754s 11 (3.53%) aligned >1 times 754s 6.09% overall alignment rate 754s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 754s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 754s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.1 754s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.2 754s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 8 754s Reference gaps introduced: 2 754s Read gaps introduced: 0 754s Rearrangements introduced: 0 754s Created read sampler 754s Sampling 44 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s *** Run 25 of 100 754s /usr/bin/bowtie2 --cp-min 2 --rdg 9.98815736872767,4.32554414713348 --score-min L,6.75864365160685,6.18212298046819 --trim3 4 --cp-ival 2 -D 31 --local --nofw -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 754s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '1' because it was < 2 characters long 754s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '2' because it was < 2 characters long 754s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '7' because it was < 2 characters long 754s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '12' because it was < 2 characters long 754s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '17' because it was < 2 characters long 754s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '21' because it was < 2 characters long 754s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '22' because it was < 2 characters long 754s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '23' because it was < 2 characters long 754s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '24' because it was < 2 characters long 754s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '30' because it was < 2 characters long 754s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '31' because it was < 2 characters long 754s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '35' because it was < 2 characters long 754s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '36' because it was < 2 characters long 754s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '38' because it was < 2 characters long 754s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '40' because it was < 2 characters long 754s 44 reads; of these: 754s 44 (100.00%) were unpaired; of these: 754s 44 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s /usr/bin/bowtie2 --cp-min 2 --rdg 9.98815736872767,4.32554414713348 --score-min L,6.75864365160685,6.18212298046819 --trim3 4 --cp-ival 2 -D 31 --local --nofw -r -p 2 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 0 alignments, 0 edits 754s --------------- 754s PASSED 754s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 754s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '1' because it was < 2 characters long 754s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '2' because it was < 2 characters long 754s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '7' because it was < 2 characters long 754s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '12' because it was < 2 characters long 754s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '17' because it was < 2 characters long 754s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '21' because it was < 2 characters long 754s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '22' because it was < 2 characters long 754s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '23' because it was < 2 characters long 754s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '24' because it was < 2 characters long 754s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '30' because it was < 2 characters long 754s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '31' because it was < 2 characters long 754s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '35' because it was < 2 characters long 754s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '36' because it was < 2 characters long 754s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 754s Warning: skipping read '38' because it was < 2 characters long 754s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 754s Warning: skipping read '40' because it was < 2 characters long 754s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 754s 44 reads; of these: 754s 44 (100.00%) were unpaired; of these: 754s 44 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 754s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.1 754s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.2 754s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 7 754s Reference gaps introduced: 1 754s Read gaps introduced: 0 754s Rearrangements introduced: 0 754s Created read sampler 754s Sampling 12 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s *** Run 26 of 100 754s /usr/bin/bowtie2 --norc -R 3 --ma 20.5811258966083 --cp-min 3 -a --score-min L,6.76174039614756,8.34527162525248 --rfg 28.1771072200752,13.1811363428815 --mp 6.76629130874517,2.91304426156392 --cp-ival 2 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 754s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '2' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 754s Warning: skipping mate #1 of read '4' because length (1) <= # seed mismatches (0) 754s Warning: skipping mate #1 of read '4' because it was < 2 characters long 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 754s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 754s 12 reads; of these: 754s 12 (100.00%) were paired; of these: 754s 12 (100.00%) aligned concordantly 0 times 754s 0 (0.00%) aligned concordantly exactly 1 time 754s 0 (0.00%) aligned concordantly >1 times 754s ---- 754s 12 pairs aligned concordantly 0 times; of these: 754s 0 (0.00%) aligned discordantly 1 time 754s ---- 754s 12 pairs aligned 0 times concordantly or discordantly; of these: 754s 24 mates make up the pairs; of these: 754s 24 (100.00%) aligned 0 times 754s 0 (0.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 0.00% overall alignment rate 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s *** Run 27 of 100 754s /usr/bin/bowtie2 -i L --np 4 --norc --cp-min 12 --ma 19.9206487677317 --mm --rfg 28.1672821143731,15.6261183033791 --score-min L,7.10114241093262,9.02912184990726 --trim3 0 --cp-ival 1 --mp 5.23101260682385,2.36430170478562 --nofw -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 754s Processing line... 754s Processing line... 754s Processing line... 754s Processing line... 754s --- Summary --- 754s Read 1 reference strings 754s Checked 0 alignments, 0 edits 754s --------------- 754s PASSED 754s Flattened IUPAC characters 754s Mutating sequence Sim.pm.2 754s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutating sequence Sim.pm.1 754s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 754s Finished SNPs 754s Finished ref gaps 754s Finished read gaps 754s Mutated reference genome to subject genome 754s SNPs introduced: 9 754s Reference gaps introduced: 1 754s Read gaps introduced: 0 754s Rearrangements introduced: 1 754s Created read sampler 754s Sampling 79 reads 754s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 754s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 754s parsing sequence Sim.pm.1... 754s parsing sequence Sim.pm.2... 754s Parsed 58 reference bases 754s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 755s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 755s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '2' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 755s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '7' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 755s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '23' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 755s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '25' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 755s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '31' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 755s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '58' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 755s 79 reads; of these: 755s 79 (100.00%) were unpaired; of these: 755s 79 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s Read 50 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 0 alignments, 0 edits 755s --------------- 755s PASSED 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.1 755s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.2 755s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 5 755s Reference gaps introduced: 1 755s Read gaps introduced: 1 755s Rearrangements introduced: 1 755s Created read sampler 755s Sampling 36 reads 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s *** Run 28 of 100 755s /usr/bin/bowtie2 --cp-min 2 --trim5 1 -M 2 --norc --trim3 5 --cp-ival 2 --local --mm --score-min L,8.72270719773607,8.55723143665338 --rfg 42.955359030145 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 755s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 755s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '10' because it was < 2 characters long 755s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '16' because it was < 2 characters long 755s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '17' because it was < 2 characters long 755s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '19' because it was < 2 characters long 755s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '22' because it was < 2 characters long 755s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '23' because it was < 2 characters long 755s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '31' because it was < 2 characters long 755s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '33' because it was < 2 characters long 755s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '36' because it was < 2 characters long 755s 36 reads; of these: 755s 36 (100.00%) were unpaired; of these: 755s 36 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s /usr/bin/bowtie2 --cp-min 2 --trim5 1 -M 2 --norc --trim3 5 --cp-ival 2 --local --mm --score-min L,8.72270719773607,8.55723143665338 --rfg 42.955359030145 -q -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 0 alignments, 0 edits 755s --------------- 755s PASSED 755s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 755s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 755s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '10' because it was < 2 characters long 755s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '16' because it was < 2 characters long 755s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '17' because it was < 2 characters long 755s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '19' because it was < 2 characters long 755s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '22' because it was < 2 characters long 755s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '23' because it was < 2 characters long 755s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '31' because it was < 2 characters long 755s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '33' because it was < 2 characters long 755s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '36' because it was < 2 characters long 755s 36 reads; of these: 755s 36 (100.00%) were unpaired; of these: 755s 36 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.2 755s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.1 755s Introducing 5 SNPs, 2/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 5 755s Reference gaps introduced: 2 755s Read gaps introduced: 0 755s Rearrangements introduced: 0 755s Created read sampler 755s Sampling 97 reads 755s *** Run 29 of 100 755s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 1.10204771052769,0.799418363697157 --cp-min 2 --nofw -i S,1.98452143961765,3.58428949334873 --trim5 4 --mm --rdg 6.46910709695616,17.9748659384733 --score-min L,4.31569953255097,2.05641522388686 -q -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 755s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '2' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 755s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '7' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 755s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '15' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 755s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '18' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 755s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '19' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 755s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '21' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 755s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '22' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 755s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #2 of read '52' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 755s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '54' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 755s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '65' because it was < 2 characters long 755s Read 50 alignments... 755s Read 100 alignments... 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 755s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '67' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 755s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '83' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 755s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '89' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 755s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '94' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 755s 97 reads; of these: 755s 91 (93.81%) were paired; of these: 755s 91 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 91 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 91 pairs aligned 0 times concordantly or discordantly; of these: 755s 182 mates make up the pairs; of these: 755s 173 (95.05%) aligned 0 times 755s 6 (3.30%) aligned exactly 1 time 755s 3 (1.65%) aligned >1 times 755s 6 (6.19%) were unpaired; of these: 755s 5 (83.33%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 1 (16.67%) aligned >1 times 755s 5.32% overall alignment rate 755s Read 150 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CTATA 755s CTATA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AAC 755s AAC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TCTC 755s TCTC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TACAACAACGC 755s TACAACAACGC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AC 755s AC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TCCTATA 755s TCCTATA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s ACA 755s ACA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s ATA 755s ATA 755s Processing line... 755s Processing line... 755s GCT 755s GCT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AC 755s AC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 10 alignments, 0 edits 755s --------------- 755s PASSED 755s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 755s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 1.10204771052769,0.799418363697157 --cp-min 2 --nofw -i S,1.98452143961765,3.58428949334873 --trim5 4 --mm --rdg 6.46910709695616,17.9748659384733 --score-min L,4.31569953255097,2.05641522388686 -q -p 2 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 755s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '2' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 755s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '7' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 755s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '15' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 755s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '18' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 755s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '19' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 755s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '21' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 755s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '22' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 755s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #2 of read '52' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 755s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '54' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 755s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '65' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 755s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '67' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 755s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '83' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 755s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read '89' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 755s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '94' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 755s 97 reads; of these: 755s 91 (93.81%) were paired; of these: 755s 91 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 91 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 91 pairs aligned 0 times concordantly or discordantly; of these: 755s 182 mates make up the pairs; of these: 755s 173 (95.05%) aligned 0 times 755s 6 (3.30%) aligned exactly 1 time 755s 3 (1.65%) aligned >1 times 755s 6 (6.19%) were unpaired; of these: 755s 5 (83.33%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 1 (16.67%) aligned >1 times 755s 5.32% overall alignment rate 755s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 755s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 755s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.1 755s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.2 755s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 9 755s Reference gaps introduced: 0 755s Read gaps introduced: 0 755s Rearrangements introduced: 1 755s Created read sampler 755s Sampling 83 reads 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s *** Run 30 of 100 755s /usr/bin/bowtie2 --cp-min 3 --np 8 -k 5 --mp 8.57168580293343,4.52861785652699 --cp-ival 1 -D 44 --local --trim3 5 --score-min L,5.72416328245489,6.41361317604646 --rdg 43.2492993996434 --gbar 3 --mm -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 755s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '3' because it was < 2 characters long 755s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '13' because it was < 2 characters long 755s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '18' because it was < 2 characters long 755s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '22' because it was < 2 characters long 755s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '40' because it was < 2 characters long 755s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '49' because it was < 2 characters long 755s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '54' because it was < 2 characters long 755s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '59' because it was < 2 characters long 755s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '62' because it was < 2 characters long 755s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '64' because it was < 2 characters long 755s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '78' because it was < 2 characters long 755s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '81' because it was < 2 characters long 755s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '82' because it was < 2 characters long 755s 83 reads; of these: 755s 83 (100.00%) were unpaired; of these: 755s 83 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s Read 50 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s /usr/bin/bowtie2 --cp-min 3 --np 8 -k 5 --mp 8.57168580293343,4.52861785652699 --cp-ival 1 -D 44 --local --trim3 5 --score-min L,5.72416328245489,6.41361317604646 --rdg 43.2492993996434 --gbar 3 --mm -f -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 0 alignments, 0 edits 755s --------------- 755s PASSED 755s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 755s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '3' because it was < 2 characters long 755s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '13' because it was < 2 characters long 755s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '18' because it was < 2 characters long 755s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '22' because it was < 2 characters long 755s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '40' because it was < 2 characters long 755s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '49' because it was < 2 characters long 755s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '54' because it was < 2 characters long 755s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '59' because it was < 2 characters long 755s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '62' because it was < 2 characters long 755s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '64' because it was < 2 characters long 755s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '78' because it was < 2 characters long 755s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '81' because it was < 2 characters long 755s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '82' because it was < 2 characters long 755s 83 reads; of these: 755s 83 (100.00%) were unpaired; of these: 755s 83 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.2 755s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.1 755s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 6 755s Reference gaps introduced: 0 755s Read gaps introduced: 0 755s Rearrangements introduced: 0 755s Created read sampler 755s Sampling 143 reads 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s *** Run 31 of 100 755s /usr/bin/bowtie2 -D 15 --cp-ival 1 -N 1 -L22 --score-min L,8.84540157246363,4.07222378912336 --rdg 16.3610002075718,5.82841797751166 --rfg 44.3863323502421,16.2482386008372 --cp-min 5 --ma 36.6625519522079 --np 3 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 755s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 755s Warning: skipping read '38' because length (1) <= # seed mismatches (1) 755s Warning: skipping read '38' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 755s Warning: skipping read '104' because length (1) <= # seed mismatches (1) 755s Warning: skipping read '104' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 755s 143 reads; of these: 755s 143 (100.00%) were unpaired; of these: 755s 116 (81.12%) aligned 0 times 755s 8 (5.59%) aligned exactly 1 time 755s 19 (13.29%) aligned >1 times 755s 18.88% overall alignment rate 755s Read 50 alignments... 755s Read 100 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TA 755s TA 755s Processing line... 755s Processing line... 755s Processing line... 755s ACAACAAC 755s ACAACAAC 755s Processing line... 755s GC 755s GC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CC 755s CC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TCTA 755s TCTA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CA 755s CA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CTA 755s CTA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AC 755s AC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AC 755s AC 755s Processing line... 755s Processing line... 755s Processing line... 755s CC 755s CC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CT 755s CT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TC 755s TC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CC 755s CC 755s Processing line... 755s Processing line... 755s CC 755s CC 755s Processing line... 755s TCTCCTA 755s TCTCCTA 755s Processing line... 755s Processing line... 755s GCA 755s GCA 755s Processing line... 755s Processing line... 755s Processing line... 755s TGCTCT 755s TGCTCT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CAA 755s CAA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CAACAACG 755s CAACAACG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s ACTGCT 755s ACTGCT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CTC 755s CTC 755s Processing line... 755s GCTCTCCTAT 755s GCTCTCCTAT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CTC 755s CTC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CA 755s CA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AC 755s AC 755s Processing line... 755s CT 755s CT 755s Processing line... 755s Processing line... 755s Processing line... 755s TAC 755s TAC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 27 alignments, 0 edits 755s --------------- 755s PASSED 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.2 755s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.1 755s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 8 755s Reference gaps introduced: 1 755s Read gaps introduced: 1 755s Rearrangements introduced: 0 755s Created read sampler 755s Sampling 103 reads 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s *** Run 32 of 100 755s /usr/bin/bowtie2 -k 4 -i L,0.251793385670724,2.95260044698186 --np 2 --gbar 4 --score-min L,3.68365815519865,1.26310241053053 --rdg 6.4069024955792 --cp-min 3 --local --cp-ival 1 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 755s Warning: skipping mate #2 of read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #2 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 755s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 755s Read 50 alignments... 755s *** Run 33 of 100 755s /usr/bin/bowtie2 --np 2 --trim5 9 --ma 33.8607700896289 --cp-min 3 -R 2 --rdg 5.16337973945182,14.6208412501828 --score-min L,2.84835269260685,1.62946907175 -a --mm --nofw -D 46 --cp-ival 1 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 755s 103 reads; of these: 755s 103 (100.00%) were paired; of these: 755s 103 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 103 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 103 pairs aligned 0 times concordantly or discordantly; of these: 755s 206 mates make up the pairs; of these: 755s 194 (94.17%) aligned 0 times 755s 11 (5.34%) aligned exactly 1 time 755s 1 (0.49%) aligned >1 times 755s 5.83% overall alignment rate 755s Read 100 alignments... 755s Read 150 alignments... 755s Read 200 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GCCTTACAACAAC 755s GCCTTACAACAAC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CCTTACAACAAC 755s CCTTACAACAAC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GCCT 755s GCCT 755s Processing line... 755s Processing line... 755s TTACAACAACG 755s TTACAACAACG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TTACAACAA 755s TTACAACAA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GCCTTACAA 755s GCCTTACAA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AGCA 755s AGCA 755s Processing line... 755s TGCT 755s TGCT 755s Processing line... 755s Processing line... 755s CCTTA 755s CCTTA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TTACAACAACGC 755s TTACAACAACGC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TTACAA 755s TTACAA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CAACAACGCG 755s CAACAACGCG 755s Processing line... 755s Processing line... 755s AACA 755s AACA 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 13 alignments, 0 edits 755s --------------- 755s PASSED 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.2 755s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.1 755s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 4 755s Reference gaps introduced: 0 755s Read gaps introduced: 1 755s Rearrangements introduced: 0 755s Created read sampler 755s Sampling 27 reads 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 755s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 755s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '0' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 755s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '3' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 755s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '8' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 755s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '10' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 755s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '15' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 755s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 755s Warning: skipping read '22' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 755s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '26' because it was < 2 characters long 755s 27 reads; of these: 755s 27 (100.00%) were unpaired; of these: 755s 27 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 0 alignments, 0 edits 755s --------------- 755s PASSED 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.1 755s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.2 755s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 0 755s Reference gaps introduced: 0 755s Read gaps introduced: 0 755s Rearrangements introduced: 1 755s Created read sampler 755s Sampling 127 reads 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s *** Run 34 of 100 755s /usr/bin/bowtie2 --trim3 8 --mp 9.55703396412911,5.35321590258896 --local --cp-ival 1 --cp-min 5 -M 5 -i S,2.18126681931675 --rfg 43.2311897280864 --score-min L,4.80138293798899,4.68424114685529 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 755s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 755s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '2' because it was < 2 characters long 755s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '5' because it was < 2 characters long 755s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '6' because it was < 2 characters long 755s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '9' because it was < 2 characters long 755s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '11' because it was < 2 characters long 755s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '16' because it was < 2 characters long 755s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '17' because it was < 2 characters long 755s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '20' because it was < 2 characters long 755s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '22' because it was < 2 characters long 755s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '23' because it was < 2 characters long 755s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '24' because it was < 2 characters long 755s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '26' because it was < 2 characters long 755s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '31' because it was < 2 characters long 755s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '32' because it was < 2 characters long 755s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '33' because it was < 2 characters long 755s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '36' because it was < 2 characters long 755s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '45' because it was < 2 characters long 755s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '48' because it was < 2 characters long 755s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '54' because it was < 2 characters long 755s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '56' because it was < 2 characters long 755s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '62' because it was < 2 characters long 755s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '67' because it was < 2 characters long 755s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '71' because it was < 2 characters long 755s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '77' because it was < 2 characters long 755s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '82' because it was < 2 characters long 755s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '86' because it was < 2 characters long 755s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '88' because it was < 2 characters long 755s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '98' because it was < 2 characters long 755s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '99' because it was < 2 characters long 755s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '102' because it was < 2 characters long 755s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '106' because it was < 2 characters long 755s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '125' because it was < 2 characters long 755s 127 reads; of these: 755s 127 (100.00%) were unpaired; of these: 755s 127 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s Read 50 alignments... 755s Read 100 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 0 alignments, 0 edits 755s --------------- 755s PASSED 755s ALSO checking that bowtie2 and bowtie2-align match up 755s /usr/bin/bowtie2 --trim3 8 --mp 9.55703396412911,5.35321590258896 --local --cp-ival 1 --cp-min 5 -M 5 -i S,2.18126681931675 --rfg 43.2311897280864 --score-min L,4.80138293798899,4.68424114685529 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 755s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 755s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '2' because it was < 2 characters long 755s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '5' because it was < 2 characters long 755s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '6' because it was < 2 characters long 755s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '9' because it was < 2 characters long 755s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '11' because it was < 2 characters long 755s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '16' because it was < 2 characters long 755s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '17' because it was < 2 characters long 755s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '20' because it was < 2 characters long 755s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '22' because it was < 2 characters long 755s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '23' because it was < 2 characters long 755s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '24' because it was < 2 characters long 755s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '26' because it was < 2 characters long 755s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '31' because it was < 2 characters long 755s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '32' because it was < 2 characters long 755s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '33' because it was < 2 characters long 755s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '36' because it was < 2 characters long 755s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '45' because it was < 2 characters long 755s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '48' because it was < 2 characters long 755s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '54' because it was < 2 characters long 755s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '56' because it was < 2 characters long 755s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '62' because it was < 2 characters long 755s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '67' because it was < 2 characters long 755s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '71' because it was < 2 characters long 755s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '77' because it was < 2 characters long 755s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '82' because it was < 2 characters long 755s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '86' because it was < 2 characters long 755s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '88' because it was < 2 characters long 755s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '98' because it was < 2 characters long 755s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '99' because it was < 2 characters long 755s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '102' because it was < 2 characters long 755s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '106' because it was < 2 characters long 755s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 755s Warning: skipping read '125' because it was < 2 characters long 755s 127 reads; of these: 755s 127 (100.00%) were unpaired; of these: 755s 127 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 0.00% overall alignment rate 755s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.1 755s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.2 755s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 3 755s Reference gaps introduced: 2 755s Read gaps introduced: 1 755s Rearrangements introduced: 0 755s Created read sampler 755s Sampling 101 reads 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s *** Run 35 of 100 755s /usr/bin/bowtie2 --trim5 4 --gbar 1 --rdg 21.3027941778943 --score-min L,4.03421038152086,1.33925042386925 --cp-ival 1 --local --n-ceil 1.0030677112568,0.321555745709799 --cp-min 3 --mp 8.02632059587038,4.11068044016503 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 755s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 755s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 755s Read 50 alignments... 755s Read 100 alignments... 755s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 755s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 755s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 755s 101 reads; of these: 755s 96 (95.05%) were paired; of these: 755s 96 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 96 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 96 pairs aligned 0 times concordantly or discordantly; of these: 755s 192 mates make up the pairs; of these: 755s 184 (95.83%) aligned 0 times 755s 8 (4.17%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 5 (4.95%) were unpaired; of these: 755s 5 (100.00%) aligned 0 times 755s 0 (0.00%) aligned exactly 1 time 755s 0 (0.00%) aligned >1 times 755s 4.06% overall alignment rate 755s Read 150 alignments... 755s Read 200 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CCTTACAACAAC 755s CCTTACAACAAC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TTACAACAACG 755s TTACAACAACG 755s Processing line... 755s Processing line... 755s TACAACAACG 755s TACAACAACG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CAACAACG 755s CAACAACG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s AACAACG 755s AACAACG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CAACGCG 755s CAACGCG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s GCCTTACA 755s GCCTTACA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CTTAC 755s CTTAC 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 8 alignments, 0 edits 755s --------------- 755s PASSED 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.1 755s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.2 755s Introducing 1 SNPs, 2/1 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 1 755s Reference gaps introduced: 2 755s Read gaps introduced: 2 755s Rearrangements introduced: 0 755s Created read sampler 755s Sampling 43 reads 755s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 755s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 755s parsing sequence Sim.pm.1... 755s parsing sequence Sim.pm.2... 755s Parsed 58 reference bases 755s *** Run 36 of 100 755s /usr/bin/bowtie2 --cp-ival 2 -D 41 --cp-min 2 --mp 5.35699625422465,1.92158092341124 --norc --rfg 43.8289566321584,10.3043154496079 --score-min L,6.46668783327028,2.67775649792017 -a --mm -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 755s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 755s Warning: skipping mate #2 of read '19' because it was < 2 characters long 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 755s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 755s 43 reads; of these: 755s 43 (100.00%) were paired; of these: 755s 43 (100.00%) aligned concordantly 0 times 755s 0 (0.00%) aligned concordantly exactly 1 time 755s 0 (0.00%) aligned concordantly >1 times 755s ---- 755s 43 pairs aligned concordantly 0 times; of these: 755s 0 (0.00%) aligned discordantly 1 time 755s ---- 755s 43 pairs aligned 0 times concordantly or discordantly; of these: 755s 86 mates make up the pairs; of these: 755s 82 (95.35%) aligned 0 times 755s 2 (2.33%) aligned exactly 1 time 755s 2 (2.33%) aligned >1 times 755s 4.65% overall alignment rate 755s Read 50 alignments... 755s Read 100 alignments... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CT 755s CT 755s Processing line... 755s CT 755s CT 755s Processing line... 755s CT 755s CT 755s Processing line... 755s CT 755s CT 755s Processing line... 755s CT 755s CT 755s Processing line... 755s CT 755s CT 755s Processing line... 755s CT 755s CT 755s Processing line... 755s CT 755s CT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s CACTG 755s CACTG 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TA 755s TA 755s Processing line... 755s TA 755s TA 755s Processing line... 755s TA 755s TA 755s Processing line... 755s TA 755s TA 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s TT 755s TT 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s Processing line... 755s --- Summary --- 755s Read 1 reference strings 755s Checked 14 alignments, 0 edits 755s --------------- 755s PASSED 755s Flattened IUPAC characters 755s Mutating sequence Sim.pm.1 755s Introducing 5 SNPs, 1/0 ref/read gaps, and 2 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutating sequence Sim.pm.2 755s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 755s Finished SNPs 755s Finished ref gaps 755s Finished read gaps 755s Mutated reference genome to subject genome 755s SNPs introduced: 6 755s Reference gaps introduced: 1 755s Read gaps introduced: 0 755s Rearrangements introduced: 2 755s Created read sampler 755s Sampling 132 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s *** Run 37 of 100 756s /usr/bin/bowtie2 --mm --score-min L,2.70420204049776,6.83477852212087 --trim3 8 --mp 7.58559006395524,5.91064548511285 --cp-ival 1 --local --trim5 2 --np 14 -R 4 --cp-min 2 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 756s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 756s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 756s Read 50 alignments... 756s 132 reads; of these: 756s 102 (77.27%) were paired; of these: 756s 102 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 102 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 102 pairs aligned 0 times concordantly or discordantly; of these: 756s 204 mates make up the pairs; of these: 756s 204 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 30 (22.73%) were unpaired; of these: 756s 30 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Read 100 alignments... 756s Read 150 alignments... 756s Read 200 alignments... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 0 alignments, 0 edits 756s --------------- 756s *** Run 38 of 100 756s /usr/bin/bowtie2 --trim3 9 --cp-min 2 --cp-ival 1 --ma 14.4161599480424 --mp 7.97284121843591,6.2669970456952 --score-min L,8.99904677547467,9.79226846496706 --rfg 7.70853260030284 --rdg 27.6120330239752,10.7558094334061 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 756s PASSED 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.1 756s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.2 756s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 12 756s Reference gaps introduced: 1 756s Read gaps introduced: 0 756s Rearrangements introduced: 0 756s Created read sampler 756s Sampling 90 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 756s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 756s *** Run 39 of 100 756s /usr/bin/bowtie2 --cp-min 2 -R 2 --trim5 6 -N 1 -L14 --mp 7.03797771466342,2.02985650465721 --cp-ival 1 --local --trim3 4 --score-min L,1.1566561587694,8.6032568962671 --rfg 14.0936554921608 --rdg 7.86561922336819,9.14515108258363 --mm -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 756s /usr/bin/bowtie2 --cp-min 2 -R 2 --trim5 6 -N 1 -L14 --mp 7.03797771466342,2.02985650465721 --cp-ival 1 --local --trim3 4 --score-min L,1.1566561587694,8.6032568962671 --rfg 14.0936554921608 --rdg 7.86561922336819,9.14515108258363 --mm -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 756s 90 reads; of these: 756s 90 (100.00%) were unpaired; of these: 756s 85 (94.44%) aligned 0 times 756s 4 (4.44%) aligned exactly 1 time 756s 1 (1.11%) aligned >1 times 756s 5.56% overall alignment rate 756s Read 50 alignments... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s TCCTA 756s TCCTA 756s Processing line... 756s Processing line... 756s Processing line... 756s CTGCTCT 756s CTGCTCT 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s CTTA 756s CTTA 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s CCT 756s CCT 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s TCC 756s TCC 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 5 alignments, 0 edits 756s --------------- 756s PASSED 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.2 756s Introducing 5 SNPs, 0/2 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.1 756s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 6 756s Reference gaps introduced: 0 756s Read gaps introduced: 3 756s Rearrangements introduced: 0 756s Created read sampler 756s Sampling 132 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '9' because it was < 2 characters long 756s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '11' because it was < 2 characters long 756s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '12' because it was < 2 characters long 756s Warning: skipping read '16' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '16' because it was < 2 characters long 756s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '18' because it was < 2 characters long 756s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '20' because it was < 2 characters long 756s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '26' because it was < 2 characters long 756s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '28' because it was < 2 characters long 756s Warning: skipping read '30' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '30' because it was < 2 characters long 756s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '31' because it was < 2 characters long 756s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '32' because it was < 2 characters long 756s Warning: skipping read '35' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '35' because it was < 2 characters long 756s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '38' because it was < 2 characters long 756s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '41' because it was < 2 characters long 756s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '44' because it was < 2 characters long 756s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '45' because it was < 2 characters long 756s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '46' because it was < 2 characters long 756s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '48' because it was < 2 characters long 756s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '49' because it was < 2 characters long 756s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '51' because it was < 2 characters long 756s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '56' because it was < 2 characters long 756s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '58' because it was < 2 characters long 756s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '67' because it was < 2 characters long 756s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '68' because it was < 2 characters long 756s Warning: skipping read '70' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '70' because it was < 2 characters long 756s Warning: skipping read '71' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '71' because it was < 2 characters long 756s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '75' because it was < 2 characters long 756s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '77' because it was < 2 characters long 756s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '83' because it was < 2 characters long 756s Warning: skipping read '86' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '86' because it was < 2 characters long 756s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '87' because it was < 2 characters long 756s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '88' because it was < 2 characters long 756s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '92' because it was < 2 characters long 756s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '93' because it was < 2 characters long 756s Warning: skipping read '96' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '96' because it was < 2 characters long 756s Warning: skipping read '97' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '97' because it was < 2 characters long 756s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '98' because it was < 2 characters long 756s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '99' because it was < 2 characters long 756s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '100' because it was < 2 characters long 756s Warning: skipping read '104' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '104' because it was < 2 characters long 756s Warning: skipping read '108' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '108' because it was < 2 characters long 756s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '110' because it was < 2 characters long 756s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '112' because it was < 2 characters long 756s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '119' because it was < 2 characters long 756s Warning: skipping read '123' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '123' because it was < 2 characters long 756s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '126' because it was < 2 characters long 756s 132 reads; of these: 756s 132 (100.00%) were unpaired; of these: 756s 132 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Read 50 alignments... 756s Read 100 alignments... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 0 alignments, 0 edits 756s --------------- 756s PASSED 756s ALSO checking that bowtie2 and bowtie2-align match up 756s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 756s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '9' because it was < 2 characters long 756s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '11' because it was < 2 characters long 756s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '12' because it was < 2 characters long 756s Warning: skipping read '16' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '16' because it was < 2 characters long 756s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '18' because it was < 2 characters long 756s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '20' because it was < 2 characters long 756s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '26' because it was < 2 characters long 756s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '28' because it was < 2 characters long 756s Warning: skipping read '30' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '30' because it was < 2 characters long 756s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '31' because it was < 2 characters long 756s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '32' because it was < 2 characters long 756s Warning: skipping read '35' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '35' because it was < 2 characters long 756s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '38' because it was < 2 characters long 756s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '41' because it was < 2 characters long 756s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '44' because it was < 2 characters long 756s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '45' because it was < 2 characters long 756s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '46' because it was < 2 characters long 756s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '48' because it was < 2 characters long 756s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '49' because it was < 2 characters long 756s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '51' because it was < 2 characters long 756s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '56' because it was < 2 characters long 756s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '58' because it was < 2 characters long 756s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '67' because it was < 2 characters long 756s Warning: skipping read '68' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '68' because it was < 2 characters long 756s Warning: skipping read '70' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '70' because it was < 2 characters long 756s Warning: skipping read '71' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '71' because it was < 2 characters long 756s Warning: skipping read '75' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '75' because it was < 2 characters long 756s Warning: skipping read '77' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '77' because it was < 2 characters long 756s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '83' because it was < 2 characters long 756s Warning: skipping read '86' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '86' because it was < 2 characters long 756s Warning: skipping read '87' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '87' because it was < 2 characters long 756s Warning: skipping read '88' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '88' because it was < 2 characters long 756s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '92' because it was < 2 characters long 756s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '93' because it was < 2 characters long 756s Warning: skipping read '96' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '96' because it was < 2 characters long 756s Warning: skipping read '97' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '97' because it was < 2 characters long 756s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '98' because it was < 2 characters long 756s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '99' because it was < 2 characters long 756s Warning: skipping read '100' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '100' because it was < 2 characters long 756s Warning: skipping read '104' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '104' because it was < 2 characters long 756s Warning: skipping read '108' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '108' because it was < 2 characters long 756s Warning: skipping read '110' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '110' because it was < 2 characters long 756s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '112' because it was < 2 characters long 756s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '119' because it was < 2 characters long 756s Warning: skipping read '123' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '123' because it was < 2 characters long 756s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '126' because it was < 2 characters long 756s 132 reads; of these: 756s 132 (100.00%) were unpaired; of these: 756s 132 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.1 756s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.2 756s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 5 756s Reference gaps introduced: 0 756s Read gaps introduced: 1 756s Rearrangements introduced: 1 756s Created read sampler 756s Sampling 42 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 756s *** Run 40 of 100 756s /usr/bin/bowtie2 -M 3 --score-min L,7.50497766859974,1.8467250726985 --trim3 3 --local --cp-ival 1 --n-ceil 1.4148748932706,0.4869962748581 --cp-min 3 -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 756s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '14' because it was < 2 characters long 756s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '17' because it was < 2 characters long 756s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '38' because it was < 2 characters long 756s 42 reads; of these: 756s 40 (95.24%) were paired; of these: 756s 40 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 40 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 40 pairs aligned 0 times concordantly or discordantly; of these: 756s 80 mates make up the pairs; of these: 756s 80 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 2 (4.76%) were unpaired; of these: 756s 2 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Read 50 alignments... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 0 alignments, 0 edits 756s --------------- 756s PASSED 756s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 756s /usr/bin/bowtie2 -M 3 --score-min L,7.50497766859974,1.8467250726985 --trim3 3 --local --cp-ival 1 --n-ceil 1.4148748932706,0.4869962748581 --cp-min 3 -f -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 756s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 756s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '14' because it was < 2 characters long 756s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '17' because it was < 2 characters long 756s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '38' because it was < 2 characters long 756s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 756s 42 reads; of these: 756s 40 (95.24%) were paired; of these: 756s 40 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 40 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 40 pairs aligned 0 times concordantly or discordantly; of these: 756s 80 mates make up the pairs; of these: 756s 80 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 2 (4.76%) were unpaired; of these: 756s 2 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.2 756s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.1 756s Introducing 5 SNPs, 0/0 ref/read gaps, and 2 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 7 756s Reference gaps introduced: 0 756s Read gaps introduced: 0 756s Rearrangements introduced: 2 756s Created read sampler 756s Sampling 1 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s *** Run 41 of 100 756s /usr/bin/bowtie2 --ma 35.6377589875877 --cp-min 3 --trim5 5 -k 3 --np 1 --mp 5.04617284234832,4.83968763769299 -N 1 -L25 --cp-ival 1 --mm --rfg 13.2374778143995 --score-min L,7.11421678481085,8.40738703293162 -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 756s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 756s 1 reads; of these: 756s 1 (100.00%) were paired; of these: 756s 1 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 1 pairs aligned concordantly 0 times; of these: 756s 1 (100.00%) aligned discordantly 1 time 756s ---- 756s 0 pairs aligned 0 times concordantly or discordantly; of these: 756s 0 mates make up the pairs; of these: 756s 0 (0.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 100.00% overall alignment rate 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s GCCTTACAAC 756s GCCTTACAAC 756s Processing line... 756s CCTTACAACAAC 756s CCTTACAACAAC 756s --- Summary --- 756s Read 1 reference strings 756s Checked 2 alignments, 0 edits 756s --------------- 756s PASSED 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.2 756s Introducing 0 SNPs, 2/1 ref/read gaps, and 1 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.1 756s Introducing 8 SNPs, 0/2 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 8 756s Reference gaps introduced: 2 756s Read gaps introduced: 3 756s Rearrangements introduced: 1 756s Created read sampler 756s Sampling 61 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s *** Run 42 of 100 756s /usr/bin/bowtie2 --trim3 2 --mp 9.17553713727773,8.457226116147 --cp-ival 1 --local --mm --rfg 40.6083913406885 --score-min L,7.35653975666775,7.80032919302023 --cp-min 9 --trim5 9 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s Warning: skipping mate #1 of read '0' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '0' because it was < 2 characters long 756s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '2' because it was < 2 characters long 756s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '3' because it was < 2 characters long 756s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '6' because it was < 2 characters long 756s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '10' because it was < 2 characters long 756s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '15' because it was < 2 characters long 756s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '22' because it was < 2 characters long 756s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '26' because it was < 2 characters long 756s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 756s Warning: skipping read '28' because it was < 2 characters long 756s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 756s Warning: skipping read '30' because it was < 2 characters long 756s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '31' because it was < 2 characters long 756s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '34' because it was < 2 characters long 756s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '35' because it was < 2 characters long 756s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '51' because it was < 2 characters long 756s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '57' because it was < 2 characters long 756s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 756s Warning: skipping read '58' because it was < 2 characters long 756s 61 reads; of these: 756s 45 (73.77%) were paired; of these: 756s 45 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 45 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 45 pairs aligned 0 times concordantly or discordantly; of these: 756s 90 mates make up the pairs; of these: 756s 90 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 16 (26.23%) were unpaired; of these: 756s 16 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Read 50 alignments... 756s Read 100 alignments... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 0 alignments, 0 edits 756s --------------- 756s PASSED 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.1 756s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.2 756s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 5 756s Reference gaps introduced: 0 756s Read gaps introduced: 0 756s Rearrangements introduced: 1 756s Created read sampler 756s Sampling 115 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s *** Run 43 of 100 756s /usr/bin/bowtie2 --mp 3.30539304248915,3.23797946713318 -D 26 --cp-ival 2 --local --mm --score-min L,2.72396432260842,7.8423666896304 --rfg 7.57734405019984 --cp-min 2 --trim5 9 -i L,0.365540611590702 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 756s Parsed 58 reference bases 756s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 756s Read 50 alignments... 756s Read 100 alignments... 756s 115 reads; of these: 756s 97 (84.35%) were paired; of these: 756s 97 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 97 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 97 pairs aligned 0 times concordantly or discordantly; of these: 756s 194 mates make up the pairs; of these: 756s 194 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 18 (15.65%) were unpaired; of these: 756s 18 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Read 150 alignments... 756s Read 200 alignments... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s 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line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 0 alignments, 0 edits 756s --------------- 756s PASSED 756s ALSO checking that bowtie2 and bowtie2-align match up 756s /usr/bin/bowtie2 --mp 3.30539304248915,3.23797946713318 -D 26 --cp-ival 2 --local --mm --score-min L,2.72396432260842,7.8423666896304 --rfg 7.57734405019984 --cp-min 2 --trim5 9 -i L,0.365540611590702 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 756s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 756s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 756s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 756s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 756s 115 reads; of these: 756s 97 (84.35%) were paired; of these: 756s 97 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 97 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 97 pairs aligned 0 times concordantly or discordantly; of these: 756s 194 mates make up the pairs; of these: 756s 194 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 18 (15.65%) were unpaired; of these: 756s 18 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.2 756s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.1 756s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 2 756s Reference gaps introduced: 0 756s Read gaps introduced: 0 756s Rearrangements introduced: 0 756s Created read sampler 756s Sampling 66 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s *** Run 44 of 100 756s /usr/bin/bowtie2 --rfg 48.1640787273397 --score-min L,9.53181661348996,3.58066225115037 --nofw --cp-ival 1 -D 19 --norc --np 5 -M 3 --ma 7.86952830660618 --cp-min 2 -R 1 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 756s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 756s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 756s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '37' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 756s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '40' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 756s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '42' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 756s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '47' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 756s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '59' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 756s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '60' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 756s Read 50 alignments... 756s Read 100 alignments... 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 756s 66 reads; of these: 756s 66 (100.00%) were paired; of these: 756s 66 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 66 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 66 pairs aligned 0 times concordantly or discordantly; of these: 756s 132 mates make up the pairs; of these: 756s 132 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 0 alignments, 0 edits 756s --------------- 756s PASSED 756s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 756s /usr/bin/bowtie2 --rfg 48.1640787273397 --score-min L,9.53181661348996,3.58066225115037 --nofw --cp-ival 1 -D 19 --norc --np 5 -M 3 --ma 7.86952830660618 --cp-min 2 -R 1 -r -p 4 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 756s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 756s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 756s Warning: skipping mate #2 of read '37' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '37' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 756s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '40' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 756s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '42' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 756s Warning: skipping mate #2 of read '47' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '47' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 756s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #1 of read '59' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 756s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 756s Warning: skipping mate #2 of read '60' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 756s 66 reads; of these: 756s 66 (100.00%) were paired; of these: 756s 66 (100.00%) aligned concordantly 0 times 756s 0 (0.00%) aligned concordantly exactly 1 time 756s 0 (0.00%) aligned concordantly >1 times 756s ---- 756s 66 pairs aligned concordantly 0 times; of these: 756s 0 (0.00%) aligned discordantly 1 time 756s ---- 756s 66 pairs aligned 0 times concordantly or discordantly; of these: 756s 132 mates make up the pairs; of these: 756s 132 (100.00%) aligned 0 times 756s 0 (0.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 0.00% overall alignment rate 756s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 756s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.1 756s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.2 756s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 3 756s Reference gaps introduced: 1 756s Read gaps introduced: 0 756s Rearrangements introduced: 0 756s Created read sampler 756s Sampling 46 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 756s *** Run 45 of 100 756s /usr/bin/bowtie2 --score-min L,2.34287619737185,7.95417240173773 --trim5 3 --mm --cp-ival 1 --cp-min 5 -N 1 -L17 --trim3 6 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 756s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 756s Warning: skipping read '4' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '4' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 756s Warning: skipping read '5' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '5' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 756s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '6' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 756s Warning: skipping read '7' because length (1) <= # seed mismatches (1) 756s Warning: skipping read '7' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 756s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '12' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 756s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '13' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 756s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '15' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 756s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '16' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 756s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '17' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 756s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '18' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 756s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '19' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 756s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '20' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 756s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '26' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 756s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '28' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 756s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '30' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 756s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '32' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 756s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '36' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 756s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '41' because it was < 2 characters long 756s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 756s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 756s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 756s Warning: skipping read '46' because it was < 2 characters long 756s 46 reads; of these: 756s 46 (100.00%) were unpaired; of these: 756s 44 (95.65%) aligned 0 times 756s 1 (2.17%) aligned exactly 1 time 756s 1 (2.17%) aligned >1 times 756s 4.35% overall alignment rate 756s Read 50 alignments... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s TAT 756s TAT 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s TCC 756s TCC 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s Processing line... 756s --- Summary --- 756s Read 1 reference strings 756s Checked 2 alignments, 0 edits 756s --------------- 756s PASSED 756s Flattened IUPAC characters 756s Mutating sequence Sim.pm.1 756s Introducing 5 SNPs, 1/0 ref/read gaps, and 2 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutating sequence Sim.pm.2 756s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 756s Finished SNPs 756s Finished ref gaps 756s Finished read gaps 756s Mutated reference genome to subject genome 756s SNPs introduced: 7 756s Reference gaps introduced: 1 756s Read gaps introduced: 0 756s Rearrangements introduced: 2 756s Created read sampler 756s Sampling 50 reads 756s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 756s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 756s parsing sequence Sim.pm.1... 756s parsing sequence Sim.pm.2... 756s Parsed 58 reference bases 756s *** Run 46 of 100 756s /usr/bin/bowtie2 --rfg 16.9311391828334,15.9461942400907 --score-min L,1.30923844002433,1.58223521825391 --n-ceil 0.810426017216505,0.583434613464373 --cp-ival 2 --local --cp-min 7 --mp 9.73719751074062,5.14655365955879 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 757s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 757s 50 reads; of these: 757s 50 (100.00%) were unpaired; of these: 757s 48 (96.00%) aligned 0 times 757s 2 (4.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 4.00% overall alignment rate 757s Read 50 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s ACTG 757s ACTG 757s Processing line... 757s CTCCTAT 757s CTCCTAT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 2 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2-align match up 757s /usr/bin/bowtie2 --rfg 16.9311391828334,15.9461942400907 --score-min L,1.30923844002433,1.58223521825391 --n-ceil 0.810426017216505,0.583434613464373 --cp-ival 2 --local --cp-min 7 --mp 9.73719751074062,5.14655365955879 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 757s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 757s 50 reads; of these: 757s 50 (100.00%) were unpaired; of these: 757s 48 (96.00%) aligned 0 times 757s 2 (4.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 4.00% overall alignment rate 757s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.2 757s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.1 757s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 7 757s Reference gaps introduced: 0 757s Read gaps introduced: 1 757s Rearrangements introduced: 0 757s Created read sampler 757s Sampling 73 reads 757s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 757s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 58 reference bases 757s *** Run 47 of 100 757s /usr/bin/bowtie2 --trim5 9 --mm --rfg 37.6631810042869,7.55818691730774 --rdg 6.64322483570972 --score-min L,5.23333930169877,8.62899140616146 --np 7 --mp 8.13227152323494,2.67479738842593 --ma 38.3470011961158 --cp-ival 1 --cp-min 6 -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 757s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '3' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 757s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '4' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 757s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '9' because it was < 2 characters long 757s Warning: skipping mate #2 of read '9' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 757s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '24' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 757s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '42' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 757s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '44' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 757s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '62' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 757s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '65' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 757s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '66' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 757s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '68' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 757s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '69' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 757s 73 reads; of these: 757s 55 (75.34%) were paired; of these: 757s 55 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 55 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 55 pairs aligned 0 times concordantly or discordantly; of these: 757s 110 mates make up the pairs; of these: 757s 103 (93.64%) aligned 0 times 757s 1 (0.91%) aligned exactly 1 time 757s 6 (5.45%) aligned >1 times 757s 18 (24.66%) were unpaired; of these: 757s 18 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 5.47% overall alignment rate 757s Read 50 alignments... 757s Read 100 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TC 757s TC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TC 757s TC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s ACA 757s ACA 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s AGC 757s AGC 757s Processing line... 757s Processing line... 757s AT 757s AT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CTA 757s CTA 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s TTACAACA 757s TTACAACA 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 7 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 757s /usr/bin/bowtie2 --trim5 9 --mm --rfg 37.6631810042869,7.55818691730774 --rdg 6.64322483570972 --score-min L,5.23333930169877,8.62899140616146 --np 7 --mp 8.13227152323494,2.67479738842593 --ma 38.3470011961158 --cp-ival 1 --cp-min 6 -f -p 2 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 757s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '3' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 757s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '4' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 757s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '9' because it was < 2 characters long 757s Warning: skipping mate #2 of read '9' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 757s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '24' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 757s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '42' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 757s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '44' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 757s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '62' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 757s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '65' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 757s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '66' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 757s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '68' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 757s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '69' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 757s 73 reads; of these: 757s 55 (75.34%) were paired; of these: 757s 55 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 55 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 55 pairs aligned 0 times concordantly or discordantly; of these: 757s 110 mates make up the pairs; of these: 757s 103 (93.64%) aligned 0 times 757s 1 (0.91%) aligned exactly 1 time 757s 6 (5.45%) aligned >1 times 757s 18 (24.66%) were unpaired; of these: 757s 18 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 5.47% overall alignment rate 757s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 757s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 757s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 757s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 757s /usr/bin/bowtie2 --trim5 9 --mm --rfg 37.6631810042869,7.55818691730774 --rdg 6.64322483570972 --score-min L,5.23333930169877,8.62899140616146 --np 7 --mp 8.13227152323494,2.67479738842593 --ma 38.3470011961158 --cp-ival 1 --cp-min 6 -f -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 757s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '3' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 757s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '4' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 757s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '9' because it was < 2 characters long 757s Warning: skipping mate #2 of read '9' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 757s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '24' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 757s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '42' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 757s Warning: skipping mate #2 of read '44' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '44' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 757s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '62' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 757s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '65' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 757s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '66' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 757s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '68' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 757s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '69' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 757s 73 reads; of these: 757s 55 (75.34%) were paired; of these: 757s 55 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 55 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 55 pairs aligned 0 times concordantly or discordantly; of these: 757s 110 mates make up the pairs; of these: 757s 103 (93.64%) aligned 0 times 757s 1 (0.91%) aligned exactly 1 time 757s 6 (5.45%) aligned >1 times 757s 18 (24.66%) were unpaired; of these: 757s 18 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 5.47% overall alignment rate 757s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.1 757s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.2 757s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 0 757s Reference gaps introduced: 0 757s Read gaps introduced: 1 757s Rearrangements introduced: 0 757s Created read sampler 757s Sampling 173 reads 757s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 757s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 58 reference bases 757s *** Run 48 of 100 757s /usr/bin/bowtie2 --trim5 3 --score-min L,5.38684013480386,7.82013785639392 --rdg 42.4224191316895,3.63499777436946 --np 3 --cp-min 2 --cp-ival 4 --local --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 757s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_159_159_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_159_159_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_162_162_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_162_162_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_167_167_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 757s 173 reads; of these: 757s 173 (100.00%) were unpaired; of these: 757s 173 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s Read 50 alignments... 757s Read 100 alignments... 757s Read 150 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s /usr/bin/bowtie2 --trim5 3 --score-min L,5.38684013480386,7.82013785639392 --rdg 42.4224191316895,3.63499777436946 --np 3 --cp-min 2 --cp-ival 4 --local --qseq -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 0 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 757s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_126_126_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_159_159_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_159_159_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_162_162_1/1' because length (1) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_162_162_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_167_167_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 757s Warning: skipping read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 757s 173 reads; of these: 757s 173 (100.00%) were unpaired; of these: 757s 173 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.1 757s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.2 757s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s *** Run 49 of 100 757s /usr/bin/bowtie2 --gbar 8 --score-min L,5.36166100145373,9.80822489769157 --mm --cp-ival 1 --n-ceil 1.31247868368434,1.20730108121438 --local --np 1 -M 3 --trim5 5 --cp-min 3 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 6 757s Reference gaps introduced: 0 757s Read gaps introduced: 1 757s Rearrangements introduced: 1 757s Created read sampler 757s Sampling 44 reads 757s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 757s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 58 reference bases 757s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 757s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '7' because it was < 2 characters long 757s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 757s Warning: skipping read '15' because it was < 2 characters long 757s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '17' because it was < 2 characters long 757s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '27' because it was < 2 characters long 757s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '30' because it was < 2 characters long 757s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '32' because it was < 2 characters long 757s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 757s Warning: skipping read '36' because it was < 2 characters long 757s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '37' because it was < 2 characters long 757s 44 reads; of these: 757s 44 (100.00%) were unpaired; of these: 757s 44 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 0 alignments, 0 edits 757s --------------- 757s PASSED 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.2 757s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.1 757s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 6 757s Reference gaps introduced: 0 757s Read gaps introduced: 1 757s Rearrangements introduced: 0 757s Created read sampler 757s Sampling 72 reads 757s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 757s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 58 reference bases 757s *** Run 50 of 100 757s /usr/bin/bowtie2 --gbar 2 --score-min L,5.94805705528001,9.90445432154397 -a --cp-ival 3 --local --nofw --mp 7.7307403712128,5.46040154301288 --trim3 7 --np 6 --norc --trim5 5 --cp-min 3 -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 757s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '3' because it was < 2 characters long 757s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '4' because it was < 2 characters long 757s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '5' because it was < 2 characters long 757s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '15' because it was < 2 characters long 757s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '27' because it was < 2 characters long 757s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '28' because it was < 2 characters long 757s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '29' because it was < 2 characters long 757s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '30' because it was < 2 characters long 757s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '33' because it was < 2 characters long 757s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '35' because it was < 2 characters long 757s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '38' because it was < 2 characters long 757s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '40' because it was < 2 characters long 757s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '42' because it was < 2 characters long 757s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '51' because it was < 2 characters long 757s Warning: skipping mate #2 of read '51' because it was < 2 characters long 757s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '52' because it was < 2 characters long 757s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '57' because it was < 2 characters long 757s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '62' because it was < 2 characters long 757s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '64' because it was < 2 characters long 757s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '65' because it was < 2 characters long 757s Warning: skipping mate #2 of read '65' because it was < 2 characters long 757s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '66' because it was < 2 characters long 757s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '67' because it was < 2 characters long 757s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '71' because it was < 2 characters long 757s 72 reads; of these: 757s 53 (73.61%) were paired; of these: 757s 53 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 53 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 53 pairs aligned 0 times concordantly or discordantly; of these: 757s 106 mates make up the pairs; of these: 757s 106 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 19 (26.39%) were unpaired; of these: 757s 19 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s Read 50 alignments... 757s Read 100 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 0 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 757s /usr/bin/bowtie2 --gbar 2 --score-min L,5.94805705528001,9.90445432154397 -a --cp-ival 3 --local --nofw --mp 7.7307403712128,5.46040154301288 --trim3 7 --np 6 --norc --trim5 5 --cp-min 3 -f -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 757s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '3' because it was < 2 characters long 757s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '4' because it was < 2 characters long 757s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '5' because it was < 2 characters long 757s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '15' because it was < 2 characters long 757s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '27' because it was < 2 characters long 757s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '28' because it was < 2 characters long 757s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '29' because it was < 2 characters long 757s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '30' because it was < 2 characters long 757s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '33' because it was < 2 characters long 757s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '35' because it was < 2 characters long 757s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '38' because it was < 2 characters long 757s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '40' because it was < 2 characters long 757s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '42' because it was < 2 characters long 757s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '51' because it was < 2 characters long 757s Warning: skipping mate #2 of read '51' because it was < 2 characters long 757s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '52' because it was < 2 characters long 757s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '57' because it was < 2 characters long 757s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '62' because it was < 2 characters long 757s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '64' because it was < 2 characters long 757s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #2 of read '65' because length (1) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '65' because it was < 2 characters long 757s Warning: skipping mate #2 of read '65' because it was < 2 characters long 757s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '66' because it was < 2 characters long 757s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 757s Warning: skipping read '67' because it was < 2 characters long 757s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 757s Warning: skipping mate #1 of read '71' because it was < 2 characters long 757s 72 reads; of these: 757s 53 (73.61%) were paired; of these: 757s 53 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 53 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 53 pairs aligned 0 times concordantly or discordantly; of these: 757s 106 mates make up the pairs; of these: 757s 106 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 19 (26.39%) were unpaired; of these: 757s 19 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.1 757s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.2 757s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 9 757s Reference gaps introduced: 1 757s Read gaps introduced: 0 757s Rearrangements introduced: 1 757s Created read sampler 757s Sampling 57 reads 757s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 757s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s *** Run 51 of 100 757s /usr/bin/bowtie2 --trim3 6 -D 37 --cp-ival 1 --cp-min 2 -N 0 -L20 -a --rdg 6.89506093416371 --score-min L,5.04217021939553,1.1110547228901 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 757s Parsed 58 reference bases 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 757s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 757s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 757s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 757s 57 reads; of these: 757s 57 (100.00%) were unpaired; of these: 757s 50 (87.72%) aligned 0 times 757s 4 (7.02%) aligned exactly 1 time 757s 3 (5.26%) aligned >1 times 757s 12.28% overall alignment rate 757s Read 50 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CG 757s CG 757s Processing line... 757s CG 757s CG 757s Processing line... 757s CG 757s CG 757s Processing line... 757s CG 757s CG 757s Processing line... 757s GCTCT 757s GCTCT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CTGC 757s CTGC 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s GCTCT 757s GCTCT 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s CAACA 757s CAACA 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s AAC 757s AAC 757s Processing line... 757s AAC 757s AAC 757s Processing line... 757s Processing line... 757s AC 757s AC 757s Processing line... 757s AC 757s AC 757s Processing line... 757s AC 757s AC 757s Processing line... 757s AC 757s AC 757s Processing line... 757s AC 757s AC 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 15 alignments, 0 edits 757s --------------- 757s PASSED 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.2 757s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.1 757s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 9 757s Reference gaps introduced: 0 757s Read gaps introduced: 1 757s Rearrangements introduced: 0 757s Created read sampler 757s Sampling 31 reads 757s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 757s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 58 reference bases 757s *** Run 52 of 100 757s /usr/bin/bowtie2 --cp-min 6 -i S,1.60092942886008 --trim5 0 --mp 9.91319699893787,6.14307235840762 -N 1 -L31 --cp-ival 1 --local --score-min L,5.28819439257333,7.49534833668946 --rfg 49.1357273690108,18.1182902725668 -a --mm -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 757s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '15' because it was < 2 characters long 757s 31 reads; of these: 757s 31 (100.00%) were paired; of these: 757s 31 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 31 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 31 pairs aligned 0 times concordantly or discordantly; of these: 757s 62 mates make up the pairs; of these: 757s 62 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s Read 50 alignments... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s Processing line... 757s --- Summary --- 757s Read 1 reference strings 757s Checked 0 alignments, 0 edits 757s --------------- 757s PASSED 757s ALSO checking that bowtie2 and bowtie2-align match up 757s /usr/bin/bowtie2 --cp-min 6 -i S,1.60092942886008 --trim5 0 --mp 9.91319699893787,6.14307235840762 -N 1 -L31 --cp-ival 1 --local --score-min L,5.28819439257333,7.49534833668946 --rfg 49.1357273690108,18.1182902725668 -a --mm -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 757s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '15' because it was < 2 characters long 757s 31 reads; of these: 757s 31 (100.00%) were paired; of these: 757s 31 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 31 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 31 pairs aligned 0 times concordantly or discordantly; of these: 757s 62 mates make up the pairs; of these: 757s 62 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 757s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 757s /usr/bin/bowtie2 --cp-min 6 -i S,1.60092942886008 --trim5 0 --mp 9.91319699893787,6.14307235840762 -N 1 -L31 --cp-ival 1 --local --score-min L,5.28819439257333,7.49534833668946 --rfg 49.1357273690108,18.1182902725668 -a --mm -f -p 4 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 757s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (1) 757s Warning: skipping mate #1 of read '15' because it was < 2 characters long 757s 31 reads; of these: 757s 31 (100.00%) were paired; of these: 757s 31 (100.00%) aligned concordantly 0 times 757s 0 (0.00%) aligned concordantly exactly 1 time 757s 0 (0.00%) aligned concordantly >1 times 757s ---- 757s 31 pairs aligned concordantly 0 times; of these: 757s 0 (0.00%) aligned discordantly 1 time 757s ---- 757s 31 pairs aligned 0 times concordantly or discordantly; of these: 757s 62 mates make up the pairs; of these: 757s 62 (100.00%) aligned 0 times 757s 0 (0.00%) aligned exactly 1 time 757s 0 (0.00%) aligned >1 times 757s 0.00% overall alignment rate 757s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 757s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 757s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 757s Flattened IUPAC characters 757s Mutating sequence Sim.pm.1 757s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutating sequence Sim.pm.2 757s Introducing 2 SNPs, 2/1 ref/read gaps, and 1 rearrangements 757s Finished SNPs 757s Finished ref gaps 757s Finished read gaps 757s Mutated reference genome to subject genome 757s SNPs introduced: 2 757s Reference gaps introduced: 2 757s Read gaps introduced: 1 757s Rearrangements introduced: 1 757s Created read sampler 757s Sampling 58 reads 757s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 757s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 757s parsing sequence Sim.pm.1... 757s parsing sequence Sim.pm.2... 757s Parsed 58 reference bases 757s *** Run 53 of 100 757s /usr/bin/bowtie2 --mm -k 2 --score-min L,3.99871003203576,5.78528310859067 --norc --np 3 --ma 18.8343346528329 --mp 9.66951790214937,2.49060868830501 --cp-min 3 --cp-ival 3 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 757s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 758s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 758s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '7' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 758s 58 reads; of these: 758s 58 (100.00%) were unpaired; of these: 758s 49 (84.48%) aligned 0 times 758s 5 (8.62%) aligned exactly 1 time 758s 4 (6.90%) aligned >1 times 758s 15.52% overall alignment rate 758s Read 50 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s AAC 758s AAC 758s Processing line... 758s AAC 758s AAC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s AG 758s AG 758s Processing line... 758s AG 758s AG 758s Processing line... 758s CTA 758s CTA 758s Processing line... 758s CTA 758s CTA 758s Processing line... 758s Processing line... 758s ACTGCTCTCCT 758s ACTGCTCTCCT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s AACA 758s AACA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s AC 758s AC 758s Processing line... 758s AC 758s AC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TCCTATA 758s TCCTATA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TG 758s TG 758s Processing line... 758s Processing line... 758s ACTGCTCTCC 758s ACTGCTCTCC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 13 alignments, 0 edits 758s /usr/bin/bowtie2 --mm -k 2 --score-min L,3.99871003203576,5.78528310859067 --norc --np 3 --ma 18.8343346528329 --mp 9.66951790214937,2.49060868830501 --cp-min 3 --cp-ival 3 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2-align match up 758s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 758s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 758s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '7' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 758s 58 reads; of these: 758s 58 (100.00%) were unpaired; of these: 758s 49 (84.48%) aligned 0 times 758s 5 (8.62%) aligned exactly 1 time 758s 4 (6.90%) aligned >1 times 758s 15.52% overall alignment rate 758s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.2 758s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.1 758s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 6 758s Reference gaps introduced: 0 758s Read gaps introduced: 0 758s Rearrangements introduced: 0 758s Created read sampler 758s Sampling 106 reads 758s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 758s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 58 reference bases 758s *** Run 54 of 100 758s /usr/bin/bowtie2 --trim5 5 -a --score-min L,1.1800858840846,6.34180115491762 --norc --cp-min 4 --cp-ival 1 --local -q -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq 758s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '4' because it was < 2 characters long 758s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '9' because it was < 2 characters long 758s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '11' because it was < 2 characters long 758s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '20' because it was < 2 characters long 758s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '22' because it was < 2 characters long 758s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '35' because it was < 2 characters long 758s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '38' because it was < 2 characters long 758s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '45' because it was < 2 characters long 758s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '48' because it was < 2 characters long 758s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '57' because it was < 2 characters long 758s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '60' because it was < 2 characters long 758s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '63' because it was < 2 characters long 758s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '70' because it was < 2 characters long 758s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '71' because it was < 2 characters long 758s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '72' because it was < 2 characters long 758s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '83' because it was < 2 characters long 758s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '98' because it was < 2 characters long 758s Read 50 alignments... 758s 106 reads; of these: 758s 94 (88.68%) were paired; of these: 758s 94 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 94 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 94 pairs aligned 0 times concordantly or discordantly; of these: 758s 188 mates make up the pairs; of these: 758s 188 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 12 (11.32%) were unpaired; of these: 758s 12 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Read 100 alignments... 758s Read 150 alignments... 758s Read 200 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 0 alignments, 0 edits 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 758s /usr/bin/bowtie2 --trim5 5 -a --score-min L,1.1800858840846,6.34180115491762 --norc --cp-min 4 --cp-ival 1 --local -q -p 2 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 758s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '4' because it was < 2 characters long 758s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '9' because it was < 2 characters long 758s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '11' because it was < 2 characters long 758s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '20' because it was < 2 characters long 758s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '22' because it was < 2 characters long 758s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '35' because it was < 2 characters long 758s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '38' because it was < 2 characters long 758s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '45' because it was < 2 characters long 758s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '48' because it was < 2 characters long 758s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '57' because it was < 2 characters long 758s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '60' because it was < 2 characters long 758s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '63' because it was < 2 characters long 758s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '70' because it was < 2 characters long 758s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '71' because it was < 2 characters long 758s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '72' because it was < 2 characters long 758s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '83' because it was < 2 characters long 758s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '98' because it was < 2 characters long 758s 106 reads; of these: 758s 94 (88.68%) were paired; of these: 758s 94 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 94 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 94 pairs aligned 0 times concordantly or discordantly; of these: 758s 188 mates make up the pairs; of these: 758s 188 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 12 (11.32%) were unpaired; of these: 758s 12 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 758s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.1 758s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.2 758s Introducing 3 SNPs, 2/1 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s *** Run 55 of 100 758s /usr/bin/bowtie2 --score-min L,6.20296980545504,9.44470780286946 -a --mm --cp-ival 1 --local -D 3 --cp-min 8 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 5 758s Reference gaps introduced: 3 758s Read gaps introduced: 2 758s Rearrangements introduced: 0 758s Created read sampler 758s Sampling 60 reads 758s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 758s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 58 reference bases 758s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '43' because it was < 2 characters long 758s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '46' because it was < 2 characters long 758s 60 reads; of these: 758s 60 (100.00%) were unpaired; of these: 758s 60 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Read 50 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 0 alignments, 0 edits 758s --------------- 758s PASSED 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.1 758s Introducing 11 SNPs, 1/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.2 758s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 12 758s Reference gaps introduced: 2 758s Read gaps introduced: 0 758s Rearrangements introduced: 0 758s Created read sampler 758s Sampling 136 reads 758s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 758s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 758s *** Run 56 of 100 758s /usr/bin/bowtie2 --cp-ival 1 --cp-min 6 -R 1 --trim3 8 --score-min L,2.66422339922701,9.85331588822038 --np 2 --mm --trim5 3 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 58 reference bases 758s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 758s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '1' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 758s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '4' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 758s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '5' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 758s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '12' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 758s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '18' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 758s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '20' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 758s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '21' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 758s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '23' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 758s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '27' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 758s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '36' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 758s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '37' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 758s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '41' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 758s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '53' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 758s Read 50 alignments... 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 758s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '65' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 758s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '69' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 758s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '71' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 758s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '73' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 758s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '74' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 758s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '76' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 758s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '77' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 758s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '84' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 758s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '85' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 758s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '90' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 758s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '91' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 758s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '93' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 758s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '96' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 758s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '99' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 758s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '100' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 758s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '101' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 758s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '102' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 758s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '103' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 758s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '104' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 758s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '119' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 758s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '124' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 758s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '127' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 758s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '128' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 758s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '135' because it was < 2 characters long 758s Read 100 alignments... 758s 136 reads; of these: 758s 108 (79.41%) were paired; of these: 758s 108 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 108 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 108 pairs aligned 0 times concordantly or discordantly; of these: 758s 216 mates make up the pairs; of these: 758s 205 (94.91%) aligned 0 times 758s 5 (2.31%) aligned exactly 1 time 758s 6 (2.78%) aligned >1 times 758s 28 (20.59%) were unpaired; of these: 758s 28 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 4.51% overall alignment rate 758s Read 150 alignments... 758s Read 200 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s /usr/bin/bowtie2 --cp-ival 1 --cp-min 6 -R 1 --trim3 8 --score-min L,2.66422339922701,9.85331588822038 --np 2 --mm --trim5 3 -r -p 2 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CTCT 758s CTCT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s ACAACAA 758s ACAACAA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TCA 758s TCA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s AT 758s AT 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TC 758s TC 758s Processing line... 758s AAC 758s AAC 758s Processing line... 758s CAAC 758s CAAC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TACAACA 758s TACAACA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CAA 758s CAA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s TACAA 758s TACAA 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s CCC 758s CCC 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 11 alignments, 0 edits 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 758s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 758s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '1' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 758s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '4' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 758s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '5' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 758s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '12' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 758s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '18' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 758s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '20' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 758s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '21' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 758s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '23' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 758s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '27' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 758s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '36' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 758s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '37' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 758s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '41' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 758s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '53' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 758s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '65' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 758s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '69' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 758s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '71' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 758s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '73' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 758s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '74' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 758s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '76' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 758s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '77' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 758s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '84' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 758s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '85' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 758s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '90' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 758s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '91' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 758s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '93' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 758s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '96' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 758s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '99' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 758s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '100' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 758s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '101' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 758s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '102' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 758s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '103' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 758s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '104' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 758s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '119' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 758s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '124' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 758s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '127' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 758s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '128' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 758s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '135' because it was < 2 characters long 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 758s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 758s /usr/bin/bowtie2 --cp-ival 1 --cp-min 6 -R 1 --trim3 8 --score-min L,2.66422339922701,9.85331588822038 --np 2 --mm --trim5 3 -r -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 758s 136 reads; of these: 758s 108 (79.41%) were paired; of these: 758s 108 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 108 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 108 pairs aligned 0 times concordantly or discordantly; of these: 758s 216 mates make up the pairs; of these: 758s 205 (94.91%) aligned 0 times 758s 5 (2.31%) aligned exactly 1 time 758s 6 (2.78%) aligned >1 times 758s 28 (20.59%) were unpaired; of these: 758s 28 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 4.51% overall alignment rate 758s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 758s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 758s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '1' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 758s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '4' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 758s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '5' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 758s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '12' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 758s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '18' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 758s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '20' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 758s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '21' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 758s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '23' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 758s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '27' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 758s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '36' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 758s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '37' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 758s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '41' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 758s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '53' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 758s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '65' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 758s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '69' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 758s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '71' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 758s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '73' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 758s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '74' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 758s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '76' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 758s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '77' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 758s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '84' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 758s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '85' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 758s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '90' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 758s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '91' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 758s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '93' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 758s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '96' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 758s Warning: skipping mate #1 of read '99' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '99' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 758s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '100' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 758s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '101' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 758s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '102' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 758s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '103' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 758s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '104' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 758s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '119' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 758s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '124' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 758s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '127' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 758s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '128' because it was < 2 characters long 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 758s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 758s Warning: skipping mate #1 of read '135' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '135' because it was < 2 characters long 758s 136 reads; of these: 758s 108 (79.41%) were paired; of these: 758s 108 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 108 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 108 pairs aligned 0 times concordantly or discordantly; of these: 758s 216 mates make up the pairs; of these: 758s 205 (94.91%) aligned 0 times 758s 5 (2.31%) aligned exactly 1 time 758s 6 (2.78%) aligned >1 times 758s 28 (20.59%) were unpaired; of these: 758s 28 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 4.51% overall alignment rate 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.2 758s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.1 758s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 8 758s Reference gaps introduced: 1 758s Read gaps introduced: 0 758s Rearrangements introduced: 0 758s Created read sampler 758s Sampling 41 reads 758s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 758s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 58 reference bases 758s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '40' because it was < 2 characters long 758s 41 reads; of these: 758s 41 (100.00%) were unpaired; of these: 758s 41 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 0 alignments, 0 edits 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 758s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 758s Warning: skipping read '40' because it was < 2 characters long 758s 41 reads; of these: 758s 41 (100.00%) were unpaired; of these: 758s 41 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.2 758s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.1 758s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 2 758s Reference gaps introduced: 0 758s Read gaps introduced: 0 758s Rearrangements introduced: 1 758s Created read sampler 758s Sampling 93 reads 758s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 758s *** Run 57 of 100 758s /usr/bin/bowtie2 --np 6 --cp-min 2 --mm --score-min L,1.8608982973622,3.02173993962253 --cp-ival 2 --local --mp 3.86958832569188,1.75782771893561 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 758s /usr/bin/bowtie2 --np 6 --cp-min 2 --mm --score-min L,1.8608982973622,3.02173993962253 --cp-ival 2 --local --mp 3.86958832569188,1.75782771893561 -r -p 3 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 758s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 758s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 758s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 58 reference bases 758s *** Run 58 of 100 758s /usr/bin/bowtie2 --cp-ival 3 --local --cp-min 6 --np 6 --rdg 36.4296309140132,8.59289569565846 --rfg 25.8073730094483 --score-min L,7.81341900217376,2.57584581568227 -M 6 --trim5 9 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '2' because it was < 2 characters long 758s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '4' because it was < 2 characters long 758s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '10' because it was < 2 characters long 758s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '13' because it was < 2 characters long 758s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '14' because it was < 2 characters long 758s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '18' because it was < 2 characters long 758s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '32' because it was < 2 characters long 758s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '45' because it was < 2 characters long 758s Warning: skipping mate #2 of read '45' because it was < 2 characters long 758s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '46' because it was < 2 characters long 758s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '49' because it was < 2 characters long 758s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '51' because it was < 2 characters long 758s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '54' because it was < 2 characters long 758s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '65' because it was < 2 characters long 758s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '66' because it was < 2 characters long 758s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '69' because it was < 2 characters long 758s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '70' because it was < 2 characters long 758s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '73' because it was < 2 characters long 758s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '77' because it was < 2 characters long 758s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '78' because it was < 2 characters long 758s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '80' because it was < 2 characters long 758s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '81' because it was < 2 characters long 758s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '83' because it was < 2 characters long 758s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '92' because it was < 2 characters long 758s Read 50 alignments... 758s 93 reads; of these: 758s 79 (84.95%) were paired; of these: 758s 79 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 79 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 79 pairs aligned 0 times concordantly or discordantly; of these: 758s 158 mates make up the pairs; of these: 758s 158 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 14 (15.05%) were unpaired; of these: 758s 14 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Read 100 alignments... 758s Read 150 alignments... 758s /usr/bin/bowtie2 --cp-ival 3 --local --cp-min 6 --np 6 --rdg 36.4296309140132,8.59289569565846 --rfg 25.8073730094483 --score-min L,7.81341900217376,2.57584581568227 -M 6 --trim5 9 -r -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 0 alignments, 0 edits 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '2' because it was < 2 characters long 758s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '4' because it was < 2 characters long 758s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '10' because it was < 2 characters long 758s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '13' because it was < 2 characters long 758s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '14' because it was < 2 characters long 758s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '18' because it was < 2 characters long 758s Warning: skipping mate #1 of read '32' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '32' because it was < 2 characters long 758s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '45' because it was < 2 characters long 758s Warning: skipping mate #2 of read '45' because it was < 2 characters long 758s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '46' because it was < 2 characters long 758s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '49' because it was < 2 characters long 758s Warning: skipping mate #1 of read '51' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '51' because it was < 2 characters long 758s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '54' because it was < 2 characters long 758s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '65' because it was < 2 characters long 758s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 758s Warning: skipping read '66' because it was < 2 characters long 758s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '69' because it was < 2 characters long 758s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '70' because it was < 2 characters long 758s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '73' because it was < 2 characters long 758s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '77' because it was < 2 characters long 758s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '78' because it was < 2 characters long 758s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '80' because it was < 2 characters long 758s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '81' because it was < 2 characters long 758s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '83' because it was < 2 characters long 758s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 758s Warning: skipping mate #1 of read '92' because it was < 2 characters long 758s 93 reads; of these: 758s 79 (84.95%) were paired; of these: 758s 79 (100.00%) aligned concordantly 0 times 758s 0 (0.00%) aligned concordantly exactly 1 time 758s 0 (0.00%) aligned concordantly >1 times 758s ---- 758s 79 pairs aligned concordantly 0 times; of these: 758s 0 (0.00%) aligned discordantly 1 time 758s ---- 758s 79 pairs aligned 0 times concordantly or discordantly; of these: 758s 158 mates make up the pairs; of these: 758s 158 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 14 (15.05%) were unpaired; of these: 758s 14 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 758s Flattened IUPAC characters 758s Mutating sequence Sim.pm.2 758s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutating sequence Sim.pm.1 758s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 758s Finished SNPs 758s Finished ref gaps 758s Finished read gaps 758s Mutated reference genome to subject genome 758s SNPs introduced: 2 758s Reference gaps introduced: 1 758s Read gaps introduced: 1 758s Rearrangements introduced: 0 758s Created read sampler 758s Sampling 70 reads 758s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 758s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 758s parsing sequence Sim.pm.1... 758s parsing sequence Sim.pm.2... 758s Parsed 58 reference bases 758s *** Run 59 of 100 758s /usr/bin/bowtie2 --np 10 -M 2 --cp-min 2 --score-min L,4.86137609380156,4.48664995486161 --mp 7.24897152425842,6.98167484693339 --cp-ival 1 -D 45 --local --trim3 3 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 758s 70 reads; of these: 758s 70 (100.00%) were unpaired; of these: 758s 70 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s Read 50 alignments... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s Processing line... 758s --- Summary --- 758s Read 1 reference strings 758s Checked 0 alignments, 0 edits 758s --------------- 758s PASSED 758s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 758s /usr/bin/bowtie2 --np 10 -M 2 --cp-min 2 --score-min L,4.86137609380156,4.48664995486161 --mp 7.24897152425842,6.98167484693339 --cp-ival 1 -D 45 --local --trim3 3 --qseq -p 4 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 758s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 758s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 758s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 758s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 758s 70 reads; of these: 758s 70 (100.00%) were unpaired; of these: 758s 70 (100.00%) aligned 0 times 758s 0 (0.00%) aligned exactly 1 time 758s 0 (0.00%) aligned >1 times 758s 0.00% overall alignment rate 758s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 759s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 759s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.2 759s Introducing 4 SNPs, 1/3 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.1 759s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 8 759s Reference gaps introduced: 1 759s Read gaps introduced: 3 759s Rearrangements introduced: 0 759s Created read sampler 759s Sampling 137 reads 759s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 759s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 58 reference bases 759s *** Run 60 of 100 759s /usr/bin/bowtie2 --cp-min 4 --norc --np 2 --trim5 3 -k 5 --mp 6.98128441367726,2.76926090446635 -N 0 -L21 --cp-ival 1 --local --rdg 28.6239425186231 --score-min L,8.51615078042858,2.01964539320667 --mm -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 759s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '35' because it was < 2 characters long 759s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '51' because it was < 2 characters long 759s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '54' because it was < 2 characters long 759s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '59' because it was < 2 characters long 759s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '60' because it was < 2 characters long 759s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '68' because it was < 2 characters long 759s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '70' because it was < 2 characters long 759s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '81' because it was < 2 characters long 759s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '92' because it was < 2 characters long 759s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '100' because it was < 2 characters long 759s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '101' because it was < 2 characters long 759s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '104' because it was < 2 characters long 759s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '105' because it was < 2 characters long 759s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '107' because it was < 2 characters long 759s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '122' because it was < 2 characters long 759s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '135' because it was < 2 characters long 759s 137 reads; of these: 759s 137 (100.00%) were unpaired; of these: 759s 137 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s Read 50 alignments... 759s Read 100 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 0 alignments, 0 edits 759s --------------- 759s PASSED 759s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 759s /usr/bin/bowtie2 --cp-min 4 --norc --np 2 --trim5 3 -k 5 --mp 6.98128441367726,2.76926090446635 -N 0 -L21 --cp-ival 1 --local --rdg 28.6239425186231 --score-min L,8.51615078042858,2.01964539320667 --mm -f -p 4 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 759s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '35' because it was < 2 characters long 759s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '51' because it was < 2 characters long 759s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '54' because it was < 2 characters long 759s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '59' because it was < 2 characters long 759s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '60' because it was < 2 characters long 759s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '68' because it was < 2 characters long 759s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '70' because it was < 2 characters long 759s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '81' because it was < 2 characters long 759s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '92' because it was < 2 characters long 759s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '100' because it was < 2 characters long 759s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '101' because it was < 2 characters long 759s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '104' because it was < 2 characters long 759s Warning: skipping read '105' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '105' because it was < 2 characters long 759s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '107' because it was < 2 characters long 759s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '122' because it was < 2 characters long 759s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '135' because it was < 2 characters long 759s 137 reads; of these: 759s 137 (100.00%) were unpaired; of these: 759s 137 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.1 759s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.2 759s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 0 759s Reference gaps introduced: 1 759s Read gaps introduced: 1 759s Rearrangements introduced: 0 759s Created read sampler 759s Sampling 122 reads 759s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 759s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 58 reference bases 759s *** Run 61 of 100 759s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --trim3 2 --rdg 23.6111311353492,3.87498613836887 --rfg 43.0949836308479 --score-min L,7.98963700240438,1.72171606046421 --trim5 7 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 759s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 759s 122 reads; of these: 759s 122 (100.00%) were unpaired; of these: 759s 122 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s Read 50 alignments... 759s Read 100 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s /usr/bin/bowtie2 --cp-ival 1 --local --cp-min 2 --trim3 2 --rdg 23.6111311353492,3.87498613836887 --rfg 43.0949836308479 --score-min L,7.98963700240438,1.72171606046421 --trim5 7 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 0 alignments, 0 edits 759s --------------- 759s PASSED 759s ALSO checking that bowtie2 and bowtie2-align match up 759s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 759s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 759s 122 reads; of these: 759s 122 (100.00%) were unpaired; of these: 759s 122 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.2 759s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.1 759s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 4 759s Reference gaps introduced: 0 759s Read gaps introduced: 0 759s Rearrangements introduced: 0 759s Created read sampler 759s Sampling 102 reads 759s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 759s *** Run 62 of 100 759s /usr/bin/bowtie2 --ma 11.652543841147 --cp-min 3 --np 8 --trim5 6 -k 14 --mp 1.70405232200606,1.05811053418526 --nofw --cp-ival 2 -D 44 --rdg 24.3871793155141,11.61240808808 --score-min L,9.10192777200782,5.65163959161815 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 759s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 58 reference bases 759s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 759s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 759s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '0' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 759s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '3' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 759s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '5' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 759s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '6' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 759s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '7' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 759s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '14' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 759s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '18' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 759s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '19' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 759s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '22' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 759s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '24' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 759s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '28' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 759s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '32' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 759s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '33' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 759s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '39' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 759s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '42' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 759s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '56' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 759s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '57' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 759s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '58' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 759s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '63' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 759s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '65' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 759s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '68' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 759s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '77' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 759s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '80' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 759s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '86' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 759s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '93' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 759s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '100' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 759s 102 reads; of these: 759s 102 (100.00%) were unpaired; of these: 759s 94 (92.16%) aligned 0 times 759s 6 (5.88%) aligned exactly 1 time 759s 2 (1.96%) aligned >1 times 759s 7.84% overall alignment rate 759s Read 50 alignments... 759s Read 100 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TTA 759s TTA 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TGC 759s TGC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s TAG 759s TAG 759s Processing line... 759s TAG 759s TAG 759s Processing line... 759s Processing line... 759s TTA 759s TTA 759s Processing line... 759s Processing line... 759s Processing line... 759s CACTGCTC 759s CACTGCTC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CCTTACAAC 759s CCTTACAAC 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CTT 759s CTT 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s AG 759s AG 759s Processing line... 759s AG 759s AG 759s Processing line... 759s AG 759s AG 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 11 alignments, 0 edits 759s --------------- 759s PASSED 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.2 759s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.1 759s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 5 759s Reference gaps introduced: 1 759s Read gaps introduced: 1 759s Rearrangements introduced: 1 759s Created read sampler 759s Sampling 115 reads 759s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 759s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 58 reference bases 759s *** Run 63 of 100 759s /usr/bin/bowtie2 --score-min L,7.2592872837742,4.0043160376916 --rdg 22.7403913447323 --mm -D 41 --cp-ival 4 --n-ceil 0.792039896977782,0.683947955554154 --local --trim3 9 --cp-min 7 -R 1 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 759s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '3' because it was < 2 characters long 759s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '11' because it was < 2 characters long 759s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '20' because it was < 2 characters long 759s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '21' because it was < 2 characters long 759s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '24' because it was < 2 characters long 759s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '25' because it was < 2 characters long 759s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '26' because it was < 2 characters long 759s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '30' because it was < 2 characters long 759s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '44' because it was < 2 characters long 759s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '53' because it was < 2 characters long 759s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '58' because it was < 2 characters long 759s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '63' because it was < 2 characters long 759s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '68' because it was < 2 characters long 759s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '69' because it was < 2 characters long 759s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '71' because it was < 2 characters long 759s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '75' because it was < 2 characters long 759s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '79' because it was < 2 characters long 759s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '80' because it was < 2 characters long 759s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '82' because it was < 2 characters long 759s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '89' because it was < 2 characters long 759s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '90' because it was < 2 characters long 759s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '93' because it was < 2 characters long 759s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '98' because it was < 2 characters long 759s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '101' because it was < 2 characters long 759s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '110' because it was < 2 characters long 759s Read 50 alignments... 759s Read 100 alignments... 759s 115 reads; of these: 759s 92 (80.00%) were paired; of these: 759s 92 (100.00%) aligned concordantly 0 times 759s 0 (0.00%) aligned concordantly exactly 1 time 759s 0 (0.00%) aligned concordantly >1 times 759s ---- 759s 92 pairs aligned concordantly 0 times; of these: 759s 0 (0.00%) aligned discordantly 1 time 759s ---- 759s 92 pairs aligned 0 times concordantly or discordantly; of these: 759s 184 mates make up the pairs; of these: 759s 184 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 23 (20.00%) were unpaired; of these: 759s 23 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s Read 150 alignments... 759s Read 200 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line...*** Run 64 of 100 759s /usr/bin/bowtie2 --score-min L,1.05337536220295,1.60915648414674 --rdg 22.3849612887584,12.7739134234295 --np 4 -R 4 --cp-min 4 --n-ceil 0.0699848953861353,1.29337915030179 --cp-ival 2 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 759s /usr/bin/bowtie2 --score-min L,1.05337536220295,1.60915648414674 --rdg 22.3849612887584,12.7739134234295 --np 4 -R 4 --cp-min 4 --n-ceil 0.0699848953861353,1.29337915030179 --cp-ival 2 --qseq -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 759s 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 0 alignments, 0 edits 759s --------------- 759s PASSED 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.1 759s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.2 759s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 5 759s Reference gaps introduced: 1 759s Read gaps introduced: 0 759s Rearrangements introduced: 0 759s Created read sampler 759s Sampling 32 reads 759s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 759s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 58 reference bases 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 759s 32 reads; of these: 759s 32 (100.00%) were unpaired; of these: 759s 25 (78.12%) aligned 0 times 759s 4 (12.50%) aligned exactly 1 time 759s 3 (9.38%) aligned >1 times 759s 21.88% overall alignment rate 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CT 759s CT 759s Processing line... 759s CTGCT 759s CTGCT 759s Processing line... 759s Processing line... 759s Processing line... 759s AA 759s AA 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CTG 759s CTG 759s Processing line... 759s Processing line... 759s Processing line... 759s TCCTATAG 759s TCCTATAG 759s Processing line... 759s Processing line... 759s ACT 759s ACT 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s CTG 759s CTG 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 7 alignments, 0 edits 759s --------------- 759s PASSED 759s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 759s 32 reads; of these: 759s 32 (100.00%) were unpaired; of these: 759s 25 (78.12%) aligned 0 times 759s 4 (12.50%) aligned exactly 1 time 759s 3 (9.38%) aligned >1 times 759s 21.88% overall alignment rate 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.2 759s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.1 759s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 2 759s Reference gaps introduced: 0 759s Read gaps introduced: 0 759s Rearrangements introduced: 0 759s Created read sampler 759s Sampling 61 reads 759s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 759s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 58 reference bases 759s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 759s *** Run 65 of 100 759s /usr/bin/bowtie2 --cp-min 3 --trim5 6 -i S,1.79464725383791 --np 1 --trim3 1 --cp-ival 2 --n-ceil 0.864266899862647,0.573854864704266 --local --mp 8.83681323944085,1.69548858567911 --mm --score-min L,6.19625546069896,7.90592859592472 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 759s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '2' because it was < 2 characters long 759s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '4' because it was < 2 characters long 759s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '7' because it was < 2 characters long 759s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '13' because it was < 2 characters long 759s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '15' because it was < 2 characters long 759s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '16' because it was < 2 characters long 759s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '19' because it was < 2 characters long 759s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '21' because it was < 2 characters long 759s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '23' because it was < 2 characters long 759s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '24' because it was < 2 characters long 759s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '27' because it was < 2 characters long 759s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '31' because it was < 2 characters long 759s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '32' because it was < 2 characters long 759s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '35' because it was < 2 characters long 759s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '37' because it was < 2 characters long 759s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '43' because it was < 2 characters long 759s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '44' because it was < 2 characters long 759s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '45' because it was < 2 characters long 759s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '48' because it was < 2 characters long 759s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '51' because it was < 2 characters long 759s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '52' because it was < 2 characters long 759s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '53' because it was < 2 characters long 759s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '54' because it was < 2 characters long 759s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '55' because it was < 2 characters long 759s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '56' because it was < 2 characters long 759s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '58' because it was < 2 characters long 759s /usr/bin/bowtie2 --cp-min 3 --trim5 6 -i S,1.79464725383791 --np 1 --trim3 1 --cp-ival 2 --n-ceil 0.864266899862647,0.573854864704266 --local --mp 8.83681323944085,1.69548858567911 --mm --score-min L,6.19625546069896,7.90592859592472 -f -p 3 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 759s 61 reads; of these: 759s 61 (100.00%) were unpaired; of these: 759s 61 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s Read 50 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 0 alignments, 0 edits 759s --------------- 759s PASSED 759s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 759s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '2' because it was < 2 characters long 759s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '4' because it was < 2 characters long 759s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '7' because it was < 2 characters long 759s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '13' because it was < 2 characters long 759s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '15' because it was < 2 characters long 759s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '16' because it was < 2 characters long 759s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '19' because it was < 2 characters long 759s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 759s Warning: skipping read '21' because it was < 2 characters long 759s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '23' because it was < 2 characters long 759s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '24' because it was < 2 characters long 759s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '27' because it was < 2 characters long 759s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '31' because it was < 2 characters long 759s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '32' because it was < 2 characters long 759s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '35' because it was < 2 characters long 759s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '37' because it was < 2 characters long 759s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '43' because it was < 2 characters long 759s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '44' because it was < 2 characters long 759s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '45' because it was < 2 characters long 759s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '48' because it was < 2 characters long 759s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '51' because it was < 2 characters long 759s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '52' because it was < 2 characters long 759s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '53' because it was < 2 characters long 759s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '54' because it was < 2 characters long 759s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '55' because it was < 2 characters long 759s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '56' because it was < 2 characters long 759s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '58' because it was < 2 characters long 759s 61 reads; of these: 759s 61 (100.00%) were unpaired; of these: 759s 61 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 759s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 759s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.2 759s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.1 759s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 4 759s Reference gaps introduced: 0 759s Read gaps introduced: 0 759s Rearrangements introduced: 0 759s Created read sampler 759s Sampling 41 reads 759s *** Run 66 of 100 759s /usr/bin/bowtie2 --trim5 5 --norc --np 8 -R 1 --cp-min 3 -a --mm --score-min L,7.24655371809242,4.14623197374387 --rfg 29.9049876969885,8.74006044394576 --gbar 2 --nofw -N 0 -L28 --local --cp-ival 1 -D 4 --n-ceil 0.0480398754977572,0.945325708413816 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 759s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 759s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 58 reference bases 759s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '1' because it was < 2 characters long 759s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '10' because it was < 2 characters long 759s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '18' because it was < 2 characters long 759s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '21' because it was < 2 characters long 759s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '25' because it was < 2 characters long 759s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '36' because it was < 2 characters long 759s 41 reads; of these: 759s 37 (90.24%) were paired; of these: 759s 37 (100.00%) aligned concordantly 0 times 759s 0 (0.00%) aligned concordantly exactly 1 time 759s 0 (0.00%) aligned concordantly >1 times 759s ---- 759s 37 pairs aligned concordantly 0 times; of these: 759s 0 (0.00%) aligned discordantly 1 time 759s ---- 759s 37 pairs aligned 0 times concordantly or discordantly; of these: 759s 74 mates make up the pairs; of these: 759s 74 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 4 (9.76%) were unpaired; of these: 759s 4 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s Read 50 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s --- Summary --- 759s Read 1 reference strings 759s Checked 0 alignments, 0 edits 759s --------------- 759s PASSED 759s ALSO checking that bowtie2 and bowtie2-align match up 759s /usr/bin/bowtie2 --trim5 5 --norc --np 8 -R 1 --cp-min 3 -a --mm --score-min L,7.24655371809242,4.14623197374387 --rfg 29.9049876969885,8.74006044394576 --gbar 2 --nofw -N 0 -L28 --local --cp-ival 1 -D 4 --n-ceil 0.0480398754977572,0.945325708413816 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 759s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '1' because it was < 2 characters long 759s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '10' because it was < 2 characters long 759s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 759s Warning: skipping read '18' because it was < 2 characters long 759s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '21' because it was < 2 characters long 759s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '25' because it was < 2 characters long 759s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read '36' because it was < 2 characters long 759s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 759s 41 reads; of these: 759s 37 (90.24%) were paired; of these: 759s 37 (100.00%) aligned concordantly 0 times 759s 0 (0.00%) aligned concordantly exactly 1 time 759s 0 (0.00%) aligned concordantly >1 times 759s ---- 759s 37 pairs aligned concordantly 0 times; of these: 759s 0 (0.00%) aligned discordantly 1 time 759s ---- 759s 37 pairs aligned 0 times concordantly or discordantly; of these: 759s 74 mates make up the pairs; of these: 759s 74 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 4 (9.76%) were unpaired; of these: 759s 4 (100.00%) aligned 0 times 759s 0 (0.00%) aligned exactly 1 time 759s 0 (0.00%) aligned >1 times 759s 0.00% overall alignment rate 759s Flattened IUPAC characters 759s Mutating sequence Sim.pm.1 759s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutating sequence Sim.pm.2 759s Introducing 1 SNPs, 0/1 ref/read gaps, and 2 rearrangements 759s Finished SNPs 759s Finished ref gaps 759s Finished read gaps 759s Mutated reference genome to subject genome 759s SNPs introduced: 4 759s Reference gaps introduced: 0 759s Read gaps introduced: 2 759s Rearrangements introduced: 2 759s Created read sampler 759s Sampling 148 reads 759s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 759s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 759s parsing sequence Sim.pm.1... 759s parsing sequence Sim.pm.2... 759s Parsed 58 reference bases 759s *** Run 67 of 100 759s /usr/bin/bowtie2 --trim5 9 -k 4 --rdg 9.19516662721949 --score-min L,7.83645523064709,8.87260366146048 --gbar 8 --np 4 --cp-ival 1 --cp-min 3 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 759s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 759s Read 50 alignments... 759s Read 100 alignments... 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 759s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 759s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 759s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 759s Read 150 alignments... 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 759s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 759s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 759s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 759s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 759s Read 200 alignments... 759s 148 reads; of these: 759s 121 (81.76%) were paired; of these: 759s 121 (100.00%) aligned concordantly 0 times 759s 0 (0.00%) aligned concordantly exactly 1 time 759s 0 (0.00%) aligned concordantly >1 times 759s ---- 759s 121 pairs aligned concordantly 0 times; of these: 759s 0 (0.00%) aligned discordantly 1 time 759s ---- 759s 121 pairs aligned 0 times concordantly or discordantly; of these: 759s 242 mates make up the pairs; of these: 759s 227 (93.80%) aligned 0 times 759s 8 (3.31%) aligned exactly 1 time 759s 7 (2.89%) aligned >1 times 759s 27 (18.24%) were unpaired; of these: 759s 24 (88.89%) aligned 0 times 759s 1 (3.70%) aligned exactly 1 time 759s 2 (7.41%) aligned >1 times 759s 6.69% overall alignment rate 759s Read 250 alignments... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s Processing line... 759s GCA 759s GCA 760s Processing line... 760s TGC 760s TGC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s AACA 760s AACA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CCTTAC 760s CCTTAC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GCCT 760s GCCT 760s Processing line... 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CCTTA 760s CCTTA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TAG 760s TAG 760s Processing line... 760s TAG 760s TAG 760s Processing line... 760s CTA 760s CTA 760s Processing line... 760s CTA 760s CTA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTCACTGCTC 760s CTCACTGCTC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GCTC 760s GCTC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTC 760s CTC 760s Processing line... 760s CTC 760s CTC 760s Processing line... 760s CTC 760s CTC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GCC 760s GCC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CA 760s CA 760s Processing line... 760s CA 760s CA 760s Processing line... 760s CA 760s CA 760s Processing line... 760s CA 760s CA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s ATCT 760s ATCT 760s Processing line... 760s Processing line... 760s CA 760s CA 760s Processing line... 760s CA 760s CA 760s Processing line... 760s CA 760s CA 760s Processing line... 760s CA 760s CA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TACA 760s TACA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s AC 760s AC 760s Processing line... 760s AC 760s AC 760s Processing line... 760s AC 760s AC 760s Processing line... 760s AC 760s AC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 42 alignments, 0 edits 760s --------------- 760s /usr/bin/bowtie2 --trim5 9 -k 4 --rdg 9.19516662721949 --score-min L,7.83645523064709,8.87260366146048 --gbar 8 --np 4 --cp-ival 1 --cp-min 3 --qseq -p 3 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 760s PASSED 760s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 760s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 760s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 760s 148 reads; of these: 760s 121 (81.76%) were paired; of these: 760s 121 (100.00%) aligned concordantly 0 times 760s 0 (0.00%) aligned concordantly exactly 1 time 760s 0 (0.00%) aligned concordantly >1 times 760s ---- 760s 121 pairs aligned concordantly 0 times; of these: 760s 0 (0.00%) aligned discordantly 1 time 760s ---- 760s 121 pairs aligned 0 times concordantly or discordantly; of these: 760s 242 mates make up the pairs; of these: 760s 227 (93.80%) aligned 0 times 760s 8 (3.31%) aligned exactly 1 time 760s 7 (2.89%) aligned >1 times 760s 27 (18.24%) were unpaired; of these: 760s 24 (88.89%) aligned 0 times 760s 1 (3.70%) aligned exactly 1 time 760s 2 (7.41%) aligned >1 times 760s 6.69% overall alignment rate 760s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 760s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 760s /usr/bin/bowtie2 --trim5 9 -k 4 --rdg 9.19516662721949 --score-min L,7.83645523064709,8.87260366146048 --gbar 8 --np 4 --cp-ival 1 --cp-min 3 --qseq -p 4 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #2 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_137_137_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_137_137_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_142_142_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 760s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_146_146_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 760s 148 reads; of these: 760s 121 (81.76%) were paired; of these: 760s 121 (100.00%) aligned concordantly 0 times 760s 0 (0.00%) aligned concordantly exactly 1 time 760s 0 (0.00%) aligned concordantly >1 times 760s ---- 760s 121 pairs aligned concordantly 0 times; of these: 760s 0 (0.00%) aligned discordantly 1 time 760s ---- 760s 121 pairs aligned 0 times concordantly or discordantly; of these: 760s 242 mates make up the pairs; of these: 760s 227 (93.80%) aligned 0 times 760s 8 (3.31%) aligned exactly 1 time 760s 7 (2.89%) aligned >1 times 760s 27 (18.24%) were unpaired; of these: 760s 24 (88.89%) aligned 0 times 760s 1 (3.70%) aligned exactly 1 time 760s 2 (7.41%) aligned >1 times 760s 6.69% overall alignment rate 760s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s Introducing 3 SNPs, 1/1 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 6 760s Reference gaps introduced: 1 760s Read gaps introduced: 1 760s Rearrangements introduced: 2 760s Created read sampler 760s Sampling 81 reads 760s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 760s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 58 reference bases 760s *** Run 68 of 100 760s /usr/bin/bowtie2 --score-min L,2.53378814802132,3.87393038639989 --rfg 16.5015612345341,16.8360445560253 -N 1 -L17 --cp-min 7 --cp-ival 1 -D 34 --local --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 760s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 760s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (1) 760s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (1) 760s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (1) 760s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 760s 81 reads; of these: 760s 81 (100.00%) were unpaired; of these: 760s 81 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s Read 50 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 0 alignments, 0 edits 760s --------------- 760s PASSED 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.1 760s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.2 760s Introducing 2 SNPs, 0/3 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 2 760s Reference gaps introduced: 0 760s Read gaps introduced: 3 760s Rearrangements introduced: 2 760s Created read sampler 760s Sampling 137 reads 760s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 760s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 58 reference bases 760s *** Run 69 of 100 760s /usr/bin/bowtie2 --cp-min 3 --trim5 8 -M 2 --np 1 --trim3 2 --cp-ival 1 --nofw --mp 9.14550989836843,4.47550333497011 --score-min L,5.67228597176462,8.73266187742179 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 760s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 760s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 760s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '2' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 760s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '3' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 760s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '10' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 760s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '14' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 760s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '16' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 760s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '18' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 760s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '19' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 760s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '20' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 760s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '23' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 760s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '26' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 760s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '29' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 760s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '33' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 760s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '35' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 760s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '39' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 760s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '40' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 760s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '42' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 760s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '43' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 760s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '48' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 760s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '57' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 760s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '60' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 760s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '62' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 760s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '63' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 760s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '69' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 760s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '70' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 760s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '73' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 760s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '75' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 760s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '76' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 760s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '78' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 760s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '79' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 760s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '81' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 760s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '84' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 760s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '86' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 760s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '87' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 760s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '89' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 760s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '94' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 760s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '97' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 760s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '98' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 760s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '100' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 760s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '101' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 760s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '103' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 760s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '111' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 760s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '112' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 760s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '113' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 760s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '116' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 760s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '119' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 760s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '128' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 760s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '130' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 760s Warning: skipping read '131' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '131' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 760s Warning: skipping read '136' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '136' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 760s 137 reads; of these: 760s 137 (100.00%) were unpaired; of these: 760s 134 (97.81%) aligned 0 times 760s 1 (0.73%) aligned exactly 1 time 760s 2 (1.46%) aligned >1 times 760s 2.19% overall alignment rate 760s Read 50 alignments... 760s Read 100 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GCT 760s GCT 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CAC 760s CAC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s AA 760s AA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 3 alignments, 0 edits 760s --------------- 760s PASSED 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.1 760s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.2 760s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 6 760s Reference gaps introduced: 0 760s Read gaps introduced: 2 760s Rearrangements introduced: 0 760s Created read sampler 760s Sampling 60 reads 760s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 760s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 58 reference bases 760s *** Run 70 of 100 760s /usr/bin/bowtie2 --cp-min 3 --ma 21.2991011428757 --cp-ival 1 --n-ceil 0.511285371593785,0.847698528112087 -N 0 -L31 --trim3 1 --gbar 2 --rdg 24.6438651390972,6.71064478038103 --score-min L,7.72961070855004,4.02483858359572 -a --mm -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 760s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 760s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 760s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '9' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 760s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '22' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 760s 60 reads; of these: 760s 60 (100.00%) were unpaired; of these: 760s 52 (86.67%) aligned 0 times 760s 3 (5.00%) aligned exactly 1 time 760s 5 (8.33%) aligned >1 times 760s 13.33% overall alignment rate 760s Read 50 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CG 760s CG 760s Processing line... 760s CG 760s CG 760s Processing line... 760s CG 760s CG 760s Processing line... 760s CG 760s CG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TT 760s TT 760s Processing line... 760s AA 760s AA 760s Processing line... 760s AA 760s AA 760s Processing line... 760s AA 760s AA 760s Processing line... 760s AA 760s AA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TAC 760s TAC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s Processing line... 760s TC 760s TC 760s Processing line... 760s TC 760s TC 760s Processing line... 760s TC 760s TC 760s Processing line... 760s TC 760s TC 760s Processing line... 760s Processing line... 760s CTG 760s CTG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTCC 760s CTCC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s Processing line... 760s GC 760s GC 760s --- Summary --- 760s Read 1 reference strings 760s Checked 31 alignments, 0 edits 760s --------------- 760s PASSED 760s ALSO checking that bowtie2 and bowtie2-align match up 760s /usr/bin/bowtie2 --cp-min 3 --ma 21.2991011428757 --cp-ival 1 --n-ceil 0.511285371593785,0.847698528112087 -N 0 -L31 --trim3 1 --gbar 2 --rdg 24.6438651390972,6.71064478038103 --score-min L,7.72961070855004,4.02483858359572 -a --mm -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 760s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 760s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 760s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '9' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 760s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '22' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 760s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 760s 60 reads; of these: 760s 60 (100.00%) were unpaired; of these: 760s 52 (86.67%) aligned 0 times 760s 3 (5.00%) aligned exactly 1 time 760s 5 (8.33%) aligned >1 times 760s 13.33% overall alignment rate 760s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 760s /usr/bin/bowtie2 --cp-min 3 --ma 21.2991011428757 --cp-ival 1 --n-ceil 0.511285371593785,0.847698528112087 -N 0 -L31 --trim3 1 --gbar 2 --rdg 24.6438651390972,6.71064478038103 --score-min L,7.72961070855004,4.02483858359572 -a --mm -q -p 4 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 760s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 760s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 760s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '9' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 760s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '22' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 760s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 760s 60 reads; of these: 760s 60 (100.00%) were unpaired; of these: 760s 52 (86.67%) aligned 0 times 760s 3 (5.00%) aligned exactly 1 time 760s 5 (8.33%) aligned >1 times 760s 13.33% overall alignment rate 760s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 760s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s Introducing 13 SNPs, 0/0 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 16 760s Reference gaps introduced: 1 760s Read gaps introduced: 1 760s Rearrangements introduced: 0 760s Created read sampler 760s Sampling 52 reads 760s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 760s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 58 reference bases 760s *** Run 71 of 100 760s /usr/bin/bowtie2 --cp-min 6 --trim5 3 --norc --np 1 -N 1 -L15 --mp 2.90398033514541,2.87715204132624 --nofw --cp-ival 1 -D 32 --local --rdg 2.29141874600695,8.17512581538674 --score-min L,9.70440531236793,5.01160624110444 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 760s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '2' because it was < 2 characters long 760s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '6' because it was < 2 characters long 760s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '8' because it was < 2 characters long 760s Warning: skipping read '25' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '25' because it was < 2 characters long 760s Warning: skipping read '27' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '27' because it was < 2 characters long 760s Warning: skipping read '30' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '30' because it was < 2 characters long 760s Warning: skipping read '33' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '33' because it was < 2 characters long 760s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '35' because it was < 2 characters long 760s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '37' because it was < 2 characters long 760s Warning: skipping read '38' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '38' because it was < 2 characters long 760s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '40' because it was < 2 characters long 760s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '44' because it was < 2 characters long 760s 52 reads; of these: 760s 52 (100.00%) were unpaired; of these: 760s 52 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s Read 50 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 0 alignments, 0 edits 760s --------------- 760s PASSED 760s ALSO checking that bowtie2 and bowtie2-align match up 760s /usr/bin/bowtie2 --cp-min 6 --trim5 3 --norc --np 1 -N 1 -L15 --mp 2.90398033514541,2.87715204132624 --nofw --cp-ival 1 -D 32 --local --rdg 2.29141874600695,8.17512581538674 --score-min L,9.70440531236793,5.01160624110444 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 760s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '2' because it was < 2 characters long 760s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '6' because it was < 2 characters long 760s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '8' because it was < 2 characters long 760s Warning: skipping read '25' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '25' because it was < 2 characters long 760s Warning: skipping read '27' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '27' because it was < 2 characters long 760s Warning: skipping read '30' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '30' because it was < 2 characters long 760s Warning: skipping read '33' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '33' because it was < 2 characters long 760s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '35' because it was < 2 characters long 760s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '37' because it was < 2 characters long 760s Warning: skipping read '38' because length (1) <= # seed mismatches (1) 760s Warning: skipping read '38' because it was < 2 characters long 760s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '40' because it was < 2 characters long 760s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 760s Warning: skipping read '44' because it was < 2 characters long 760s 52 reads; of these: 760s 52 (100.00%) were unpaired; of these: 760s 52 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 2 760s Reference gaps introduced: 0 760s Read gaps introduced: 1 760s Rearrangements introduced: 1 760s Created read sampler 760s Sampling 94 reads 760s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 760s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 58 reference bases 760s *** Run 72 of 100 760s /usr/bin/bowtie2 --trim5 0 --gbar 1 --score-min L,1.75565780756572,2.08320702289818 --rfg 47.3275563492637,16.3923568759814 --rdg 39.6509844327037 --cp-min 3 --cp-ival 2 --mp 5.30294660979438,3.38726481046412 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 760s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 760s 94 reads; of these: 760s 94 (100.00%) were unpaired; of these: 760s 85 (90.43%) aligned 0 times 760s 3 (3.19%) aligned exactly 1 time 760s 6 (6.38%) aligned >1 times 760s 9.57% overall alignment rate 760s Read 50 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TCCTATA 760s TCCTATA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTAGCAC 760s CTAGCAC 760s Processing line... 760s Processing line... 760s CTATA 760s CTATA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s ACTGCTCTC 760s ACTGCTCTC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s AA 760s AA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s ATAG 760s ATAG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TG 760s TG 760s Processing line... 760s Processing line... 760s Processing line... 760s ACA 760s ACA 760s Processing line... 760s CTA 760s CTA 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 9 alignments, 0 edits 760s --------------- 760s PASSED 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s *** Run 73 of 100 760s /usr/bin/bowtie2 --rdg 17.9597029865602,12.79876546324 --score-min L,1.32311235110487,4.16713132392902 --trim5 6 -k 6 --mp 7.56375049889032,5.36072900503034 --ma 36.6435863658343 --nofw --cp-ival 1 --cp-min 2 -R 2 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 760s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 6 760s Reference gaps introduced: 0 760s Read gaps introduced: 0 760s Rearrangements introduced: 1 760s Created read sampler 760s Sampling 144 reads 760s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 760s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 58 reference bases 760s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 760s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 760s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '2' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 760s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '6' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 760s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '10' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 760s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '11' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 760s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '12' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 760s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '13' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 760s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '15' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 760s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '23' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 760s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '29' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 760s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '31' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 760s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '32' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 760s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '34' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 760s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '35' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 760s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '37' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 760s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '38' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 760s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '40' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 760s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '41' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 760s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '42' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 760s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '46' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 760s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '48' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 760s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '52' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 760s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '58' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 760s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '61' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 760s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '77' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 760s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '81' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 760s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '82' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 760s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '86' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 760s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '89' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 760s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '90' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 760s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '98' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 760s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '103' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 760s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '105' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 760s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '113' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 760s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '115' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 760s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '125' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 760s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '126' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 760s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '128' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 760s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '129' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 760s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 760s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '138' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 760s Warning: skipping read '139' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '139' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 760s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '140' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 760s Warning: skipping read '141' because length (0) <= # seed mismatches (0) 760s Warning: skipping read '141' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 760s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 760s Warning: skipping read '142' because it was < 2 characters long 760s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 760s 144 reads; of these: 760s 144 (100.00%) were unpaired; of these: 760s 134 (93.06%) aligned 0 times 760s 7 (4.86%) aligned exactly 1 time 760s 3 (2.08%) aligned >1 times 760s 6.94% overall alignment rate 760s Read 50 alignments... 760s Read 100 alignments... 760s Read 150 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s CC 760s CC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CCC 760s CCC 760s Processing line... 760s CCC 760s CCC 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s AACA 760s AACA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s TCACTGC 760s TCACTGC 760s Processing line... 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s CT 760s CT 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTTACA 760s CTTACA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s CTAG 760s CTAG 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s ATA 760s ATA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s AAA 760s AAA 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s GCA 760s GCA 760s --- Summary --- 760s Read 1 reference strings 760s Checked 20 alignments, 0 edits 760s --------------- 760s PASSED 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.1 760s Introducing 5 SNPs, 2/1 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s *** Run 74 of 100 760s /usr/bin/bowtie2 --cp-min 3 --local --cp-ival 3 -R 4 --score-min L,2.94340469790129,7.27647075173446 --norc --mm -a --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 760s Mutating sequence Sim.pm.2 760s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 6 760s Reference gaps introduced: 2 760s Read gaps introduced: 1 760s Rearrangements introduced: 1 760s Created read sampler 760s Sampling 83 reads 760s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 760s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 58 reference bases 760s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 760s 83 reads; of these: 760s 83 (100.00%) were unpaired; of these: 760s 83 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s Read 50 alignments... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 0 alignments, 0 edits 760s --------------- 760s PASSED 760s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 760s /usr/bin/bowtie2 --cp-min 3 --local --cp-ival 3 -R 4 --score-min L,2.94340469790129,7.27647075173446 --norc --mm -a --qseq -p 4 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 760s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 760s 83 reads; of these: 760s 83 (100.00%) were unpaired; of these: 760s 83 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 760s Flattened IUPAC characters 760s Mutating sequence Sim.pm.2 760s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutating sequence Sim.pm.1 760s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 760s Finished SNPs 760s Finished ref gaps 760s Finished read gaps 760s Mutated reference genome to subject genome 760s SNPs introduced: 5 760s Reference gaps introduced: 0 760s Read gaps introduced: 0 760s Rearrangements introduced: 0 760s Created read sampler 760s Sampling 44 reads 760s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 760s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 760s parsing sequence Sim.pm.1... 760s parsing sequence Sim.pm.2... 760s Parsed 58 reference bases 760s *** Run 75 of 100 760s /usr/bin/bowtie2 --local --cp-ival 2 -D 47 --trim3 8 --score-min L,4.82258622437708,1.78871700309261 --mm --cp-min 5 --np 2 -k 12 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 760s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 760s 44 reads; of these: 760s 44 (100.00%) were unpaired; of these: 760s 44 (100.00%) aligned 0 times 760s 0 (0.00%) aligned exactly 1 time 760s 0 (0.00%) aligned >1 times 760s 0.00% overall alignment rate 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s Processing line... 760s --- Summary --- 760s Read 1 reference strings 760s Checked 0 alignments, 0 edits 760s --------------- 760s PASSED 760s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 760s /usr/bin/bowtie2 --local --cp-ival 2 -D 47 --trim3 8 --score-min L,4.82258622437708,1.78871700309261 --mm --cp-min 5 --np 2 -k 12 --qseq -p 4 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 760s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 760s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 760s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 761s 44 reads; of these: 761s 44 (100.00%) were unpaired; of these: 761s 44 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 761s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 7 761s Reference gaps introduced: 0 761s Read gaps introduced: 0 761s Rearrangements introduced: 1 761s Created read sampler 761s Sampling 48 reads 761s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 761s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 58 reference bases 761s *** Run 76 of 100 761s /usr/bin/bowtie2 --cp-min 3 --np 3 --cp-ival 2 --local --score-min L,8.39858701912682,7.73504695551423 --rdg 24.7481180176093,13.5944379640404 --gbar 2 --mm -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 761s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '9' because it was < 2 characters long 761s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '14' because it was < 2 characters long 761s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '40' because it was < 2 characters long 761s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '42' because it was < 2 characters long 761s 48 reads; of these: 761s 48 (100.00%) were unpaired; of these: 761s 48 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s Read 50 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 0 alignments, 0 edits 761s --------------- 761s PASSED 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.1 761s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.2 761s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 4 761s Reference gaps introduced: 1 761s Read gaps introduced: 0 761s Rearrangements introduced: 1 761s Created read sampler 761s Sampling 96 reads 761s *** Run 77 of 100 761s /usr/bin/bowtie2 -R 3 --cp-min 2 --trim5 8 --np 5 --mp 9.6965790410569,1.27442769907711 --cp-ival 3 --local --mm --score-min L,7.08144901549591,1.88223026692382 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 761s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 761s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 58 reference bases 761s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 761s 96 reads; of these: 761s 96 (100.00%) were unpaired; of these: 761s 96 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s Read 50 alignments... 761s Read 100 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 0 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2-align match up 761s /usr/bin/bowtie2 -R 3 --cp-min 2 --trim5 8 --np 5 --mp 9.6965790410569,1.27442769907711 --cp-ival 3 --local --mm --score-min L,7.08144901549591,1.88223026692382 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 761s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 761s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 761s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 761s 96 reads; of these: 761s 96 (100.00%) were unpaired; of these: 761s 96 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.1 761s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.2 761s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 6 761s Reference gaps introduced: 0 761s Read gaps introduced: 0 761s Rearrangements introduced: 0 761s Created read sampler 761s Sampling 25 reads 761s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 761s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 58 reference bases 761s *** Run 78 of 100 761s /usr/bin/bowtie2 --mp 5.10038475623946,4.33969747129562 --cp-ival 3 --local --cp-min 3 --rdg 41.1537636211468 --score-min L,2.76670851426675,6.09598077515064 --gbar 1 -a -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 761s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '7' because it was < 2 characters long 761s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '10' because it was < 2 characters long 761s 25 reads; of these: 761s 25 (100.00%) were paired; of these: 761s 25 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 25 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 25 pairs aligned 0 times concordantly or discordantly; of these: 761s 50 mates make up the pairs; of these: 761s 50 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s Read 50 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s /usr/bin/bowtie2 --mp 5.10038475623946,4.33969747129562 --cp-ival 3 --local --cp-min 3 --rdg 41.1537636211468 --score-min L,2.76670851426675,6.09598077515064 --gbar 1 -a -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 0 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2-align match up 761s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '7' because it was < 2 characters long 761s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '10' because it was < 2 characters long 761s 25 reads; of these: 761s 25 (100.00%) were paired; of these: 761s 25 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 25 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 25 pairs aligned 0 times concordantly or discordantly; of these: 761s 50 mates make up the pairs; of these: 761s 50 (100.00%) aligned 0 times 761s 0 (0.00%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 0.00% overall alignment rate 761s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.1 761s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.2 761s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 2 761s Reference gaps introduced: 1 761s Read gaps introduced: 2 761s Rearrangements introduced: 0 761s Created read sampler 761s Sampling 47 reads 761s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 761s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 761s parsing sequence Sim.pm.1... 761s *** Run 79 of 100 761s /usr/bin/bowtie2 --np 6 --cp-min 7 -R 3 --rdg 35.863484573735,6.44777152643566 --rfg 31.5193789927974,18.5811018666223 --score-min L,1.83298580013392,5.26168928818944 -a --mm -D 20 --cp-ival 1 --trim3 1 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 761s parsing sequence Sim.pm.2... 761s Parsed 58 reference bases 761s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 761s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '3' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 761s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '19' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 761s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '32' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 761s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '36' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 761s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '45' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 761s 47 reads; of these: 761s 47 (100.00%) were unpaired; of these: 761s 38 (80.85%) aligned 0 times 761s 1 (2.13%) aligned exactly 1 time 761s 8 (17.02%) aligned >1 times 761s 19.15% overall alignment rate 761s Read 50 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s Processing line... 761s Processing line... 761s ACG 761s ACG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CC 761s CC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s Processing line... 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s AG 761s AG 761s /usr/bin/bowtie2 --np 6 --cp-min 7 -R 3 --rdg 35.863484573735,6.44777152643566 --rfg 31.5193789927974,18.5811018666223 --score-min L,1.83298580013392,5.26168928818944 -a --mm -D 20 --cp-ival 1 --trim3 1 -q -p 2 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s Processing line... 761s Processing line... 761s CTA 761s CTA 761s Processing line... 761s TAG 761s TAG 761s Processing line... 761s CTA 761s CTA 761s Processing line... 761s TAG 761s TAG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TA 761s TA 761s Processing line... 761s TA 761s TA 761s Processing line... 761s TA 761s TA 761s Processing line... 761s TA 761s TA 761s Processing line... 761s TA 761s TA 761s Processing line... 761s TA 761s TA 761s Processing line... 761s TA 761s TA 761s Processing line... 761s TA 761s TA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s AG 761s AG 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s Processing line... 761s Processing line... 761s CAC 761s CAC 761s Processing line... 761s CAC 761s CAC 761s Processing line... 761s Processing line... 761s ACAAC 761s ACAAC 761s Processing line... 761s ACAAC 761s ACAAC 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 55 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 761s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 761s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '3' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 761s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '19' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 761s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '32' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 761s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '36' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 761s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '45' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 761s 47 reads; of these: 761s 47 (100.00%) were unpaired; of these: 761s 38 (80.85%) aligned 0 times 761s 1 (2.13%) aligned exactly 1 time 761s 8 (17.02%) aligned >1 times 761s 19.15% overall alignment rate 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 761s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 761s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 761s /usr/bin/bowtie2 --np 6 --cp-min 7 -R 3 --rdg 35.863484573735,6.44777152643566 --rfg 31.5193789927974,18.5811018666223 --score-min L,1.83298580013392,5.26168928818944 -a --mm -D 20 --cp-ival 1 --trim3 1 -q -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 761s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 761s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '3' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 761s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '19' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 761s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '32' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 761s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '36' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 761s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '45' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 761s 47 reads; of these: 761s 47 (100.00%) were unpaired; of these: 761s 38 (80.85%) aligned 0 times 761s 1 (2.13%) aligned exactly 1 time 761s 8 (17.02%) aligned >1 times 761s 19.15% overall alignment rate 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 761s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 3 761s Reference gaps introduced: 0 761s Read gaps introduced: 0 761s Rearrangements introduced: 0 761s Created read sampler 761s Sampling 102 reads 761s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 761s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 58 reference bases 761s *** Run 80 of 100 761s /usr/bin/bowtie2 --n-ceil 0.906055600622076,1.1575536031239 --cp-ival 3 --trim3 3 --rdg 41.6189569815115,14.7750026792638 --rfg 29.0647875412865,16.7080620625919 --score-min L,5.67633568425129,4.1793750050696 --mm --cp-min 7 --ma 12.4265199565581 -R 2 --trim5 1 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 761s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 761s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 761s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '2' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 761s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '5' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 761s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '7' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 761s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '10' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 761s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '16' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 761s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '17' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 761s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '19' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 761s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '39' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 761s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '41' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 761s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '44' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 761s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '48' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 761s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '57' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 761s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '58' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 761s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '67' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 761s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '73' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 761s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '74' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 761s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '76' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 761s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '80' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 761s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '82' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 761s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '85' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 761s Warning: skipping read '90' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '90' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 761s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 761s Warning: skipping read '99' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 761s 102 reads; of these: 761s 102 (100.00%) were unpaired; of these: 761s 92 (90.20%) aligned 0 times 761s 6 (5.88%) aligned exactly 1 time 761s 4 (3.92%) aligned >1 times 761s 9.80% overall alignment rate 761s Read 50 alignments... 761s Read 100 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TCA 761s TCA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s AA 761s AA 761s Processing line... 761s Processing line... 761s AA 761s AA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TAGCA 761s TAGCA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TCA 761s TCA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TC 761s TC 761s Processing line... 761s Processing line... 761s CTCC 761s CTCC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CCTTACAA 761s CCTTACAA 761s Processing line... 761s CTG 761s CTG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TG 761s TG 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 10 alignments, 0 edits 761s --------------- 761s PASSED 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 7 761s Reference gaps introduced: 0 761s Read gaps introduced: 1 761s Rearrangements introduced: 0 761s Created read sampler 761s Sampling 144 reads 761s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 761s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 58 reference bases 761s *** Run 81 of 100 761s /usr/bin/bowtie2 --cp-min 2 -a --rfg 19.8518742026805 --rdg 25.9182903953151 --score-min L,4.82623660621704,1.24719929509421 --mp 8.26597010093157,3.11582602273916 --cp-ival 1 -D 25 --local -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 761s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '6' because it was < 2 characters long 761s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '54' because it was < 2 characters long 761s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '71' because it was < 2 characters long 761s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '110' because it was < 2 characters long 761s Warning: skipping read '141' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '141' because it was < 2 characters long 761s 144 reads; of these: 761s 144 (100.00%) were unpaired; of these: 761s 138 (95.83%) aligned 0 times 761s 6 (4.17%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 4.17% overall alignment rate 761s Read 50 alignments... 761s Read 100 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TCACTGCT 761s TCACTGCT 761s Processing line... 761s Processing line... 761s TAGCACT 761s TAGCACT 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TGCTCT 761s TGCTCT 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TTACAACAACG 761s TTACAACAACG 761s Processing line... 761s ACTGCTCTCCTATAG 761s ACTGCTCTCCTATAG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TGCTCTCCTATAG 761s TGCTCTCCTATAG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 6 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 761s /usr/bin/bowtie2 --cp-min 2 -a --rfg 19.8518742026805 --rdg 25.9182903953151 --score-min L,4.82623660621704,1.24719929509421 --mp 8.26597010093157,3.11582602273916 --cp-ival 1 -D 25 --local -r -p 2 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 761s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '6' because it was < 2 characters long 761s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '54' because it was < 2 characters long 761s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '71' because it was < 2 characters long 761s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '110' because it was < 2 characters long 761s Warning: skipping read '141' because length (1) <= # seed mismatches (0) 761s Warning: skipping read '141' because it was < 2 characters long 761s 144 reads; of these: 761s 144 (100.00%) were unpaired; of these: 761s 138 (95.83%) aligned 0 times 761s 6 (4.17%) aligned exactly 1 time 761s 0 (0.00%) aligned >1 times 761s 4.17% overall alignment rate 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 761s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.1 761s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.2 761s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 7 761s Reference gaps introduced: 1 761s Read gaps introduced: 0 761s Rearrangements introduced: 0 761s Created read sampler 761s Sampling 44 reads 761s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 761s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 58 reference bases 761s *** Run 82 of 100 761s /usr/bin/bowtie2 --cp-ival 3 -a --mm --rdg 12.3436482256325,16.0717033171536 --score-min L,8.99059706237202,2.03475700130423 --cp-min 2 -i C,3.68347194888402 --trim5 0 --np 10 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 761s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '3' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 761s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '17' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 761s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '18' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 761s 44 reads; of these: 761s 44 (100.00%) were paired; of these: 761s 44 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 44 pairs aligned concordantly 0 times; of these: 761s 1 (2.27%) aligned discordantly 1 time 761s ---- 761s 43 pairs aligned 0 times concordantly or discordantly; of these: 761s 86 mates make up the pairs; of these: 761s 78 (90.70%) aligned 0 times 761s 1 (1.16%) aligned exactly 1 time 761s 7 (8.14%) aligned >1 times 761s 11.36% overall alignment rate 761s Read 50 alignments... 761s Read 100 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CAACG 761s CAACG 761s Processing line... 761s CTG 761s CTG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CC 761s CC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s CC 761s CC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s AAC 761s AAC 761s Processing line... 761s AAC 761s AAC 761s Processing line... 761s Processing line... 761s ATA 761s ATA 761s Processing line... 761s TAT 761s TAT 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s /usr/bin/bowtie2 --cp-ival 3 -a --mm --rdg 12.3436482256325,16.0717033171536 --score-min L,8.99059706237202,2.03475700130423 --cp-min 2 -i C,3.68347194888402 --trim5 0 --np 10 -r -p 3 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 761s Processing line... 761s Processing line... 761s AC 761s AC 761s Processing line... 761s AC 761s AC 761s Processing line... 761s AC 761s AC 761s Processing line... 761s AC 761s AC 761s Processing line... 761s AC 761s AC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s AA 761s AA 761s Processing line... 761s TT 761s TT 761s Processing line... 761s AA 761s AA 761s Processing line... 761s AA 761s AA 761s Processing line... 761s AA 761s AA 761s Processing line... 761s Processing line... 761s CG 761s CG 761s Processing line... 761s CG 761s CG 761s Processing line... 761s CG 761s CG 761s Processing line... 761s CG 761s CG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s CT 761s CT 761s Processing line... 761s AG 761s AG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TTACAA 761s TTACAA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 37 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 761s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '3' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 761s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #2 of read '17' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 761s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 761s Warning: skipping mate #1 of read '18' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 761s 44 reads; of these: 761s 44 (100.00%) were paired; of these: 761s 44 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 44 pairs aligned concordantly 0 times; of these: 761s 1 (2.27%) aligned discordantly 1 time 761s ---- 761s 43 pairs aligned 0 times concordantly or discordantly; of these: 761s 86 mates make up the pairs; of these: 761s 78 (90.70%) aligned 0 times 761s 1 (1.16%) aligned exactly 1 time 761s 7 (8.14%) aligned >1 times 761s 11.36% overall alignment rate 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 761s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 761s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 761s Flattened IUPAC characters 761s Mutating sequence Sim.pm.2 761s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutating sequence Sim.pm.1 761s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 761s Finished SNPs 761s Finished ref gaps 761s Finished read gaps 761s Mutated reference genome to subject genome 761s SNPs introduced: 4 761s Reference gaps introduced: 0 761s Read gaps introduced: 1 761s Rearrangements introduced: 1 761s Created read sampler 761s Sampling 131 reads 761s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 761s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 761s parsing sequence Sim.pm.1... 761s parsing sequence Sim.pm.2... 761s Parsed 58 reference bases 761s *** Run 83 of 100 761s /usr/bin/bowtie2 -R 2 --cp-min 4 --cp-ival 2 --mp 6.52298836664018,4.73043328900208 -N 1 -L30 --mm --gbar 3 --rfg 35.2972833347829,1.10615252518233 --score-min L,6.2010884369223,7.57326451676315 -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 761s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #2 of read '13' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 761s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #2 of read '20' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 761s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #1 of read '35' because it was < 2 characters long 761s Warning: skipping mate #2 of read '35' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 761s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #1 of read '49' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 761s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #1 of read '52' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 761s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #2 of read '75' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 761s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #1 of read '89' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 761s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #2 of read '93' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 761s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (1) 761s Warning: skipping mate #1 of read '96' because it was < 2 characters long 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 761s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 761s Read 50 alignments... 761s 131 reads; of these: 761s 131 (100.00%) were paired; of these: 761s 131 (100.00%) aligned concordantly 0 times 761s 0 (0.00%) aligned concordantly exactly 1 time 761s 0 (0.00%) aligned concordantly >1 times 761s ---- 761s 131 pairs aligned concordantly 0 times; of these: 761s 0 (0.00%) aligned discordantly 1 time 761s ---- 761s 131 pairs aligned 0 times concordantly or discordantly; of these: 761s 262 mates make up the pairs; of these: 761s 242 (92.37%) aligned 0 times 761s 9 (3.44%) aligned exactly 1 time 761s 11 (4.20%) aligned >1 times 761s 7.63% overall alignment rate 761s Read 100 alignments... 761s Read 150 alignments... 761s Read 200 alignments... 761s Read 250 alignments... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TG 761s TG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s /usr/bin/bowtie2 -R 2 --cp-min 4 --cp-ival 2 --mp 6.52298836664018,4.73043328900208 -N 1 -L30 --mm --gbar 3 --rfg 35.2972833347829,1.10615252518233 --score-min L,6.2010884369223,7.57326451676315 -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s GCA 761s GCA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TTACAACAAC 761s TTACAACAAC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TCTC 761s TCTC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TTACAACAACGC 761s TTACAACAACGC 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TACAACAACG 761s TACAACAACG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TACAAC 761s TACAAC 761s Processing line... 761s Processing line... 761s CACT 761s CACT 761s Processing line... 761s Processing line... 761s CA 761s CA 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s AACGCG 761s AACGCG 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s ACAACGCG 761s ACAACGCG 761s Processing line... 761s Processing line... 761s GCT 761s GCT 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s Processing line... 761s TGC 761s TGC 761s 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Processing line... 761s CA 761s CA 761s Processing line... 761s --- Summary --- 761s Read 1 reference strings 761s Checked 20 alignments, 0 edits 761s --------------- 761s PASSED 761s ALSO checking that bowtie2 and bowtie2-align match up 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '13' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '20' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 762s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '35' because it was < 2 characters long 762s Warning: skipping mate #2 of read '35' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 762s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '49' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '52' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '75' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 762s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '89' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 762s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '93' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 762s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '96' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 762s 131 reads; of these: 762s 131 (100.00%) were paired; of these: 762s 131 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 131 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 131 pairs aligned 0 times concordantly or discordantly; of these: 762s 262 mates make up the pairs; of these: 762s 242 (92.37%) aligned 0 times 762s 9 (3.44%) aligned exactly 1 time 762s 11 (4.20%) aligned >1 times 762s 7.63% overall alignment rate 762s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 762s /usr/bin/bowtie2 -R 2 --cp-min 4 --cp-ival 2 --mp 6.52298836664018,4.73043328900208 -N 1 -L30 --mm --gbar 3 --rfg 35.2972833347829,1.10615252518233 --score-min L,6.2010884369223,7.57326451676315 -f -p 2 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '13' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '20' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 762s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '35' because it was < 2 characters long 762s Warning: skipping mate #2 of read '35' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 762s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '49' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '52' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '75' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 762s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '89' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 762s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '93' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 762s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '96' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 762s 131 reads; of these: 762s 131 (100.00%) were paired; of these: 762s 131 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 131 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 131 pairs aligned 0 times concordantly or discordantly; of these: 762s 262 mates make up the pairs; of these: 762s 242 (92.37%) aligned 0 times 762s 9 (3.44%) aligned exactly 1 time 762s 11 (4.20%) aligned >1 times 762s 7.63% overall alignment rate 762s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 762s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 762s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 762s /usr/bin/bowtie2 -R 2 --cp-min 4 --cp-ival 2 --mp 6.52298836664018,4.73043328900208 -N 1 -L30 --mm --gbar 3 --rfg 35.2972833347829,1.10615252518233 --score-min L,6.2010884369223,7.57326451676315 -f -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 762s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '13' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '20' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 762s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '35' because it was < 2 characters long 762s Warning: skipping mate #2 of read '35' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 762s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '49' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '52' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '75' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 762s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '89' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 762s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #2 of read '93' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 762s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (1) 762s Warning: skipping mate #1 of read '96' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 762s 131 reads; of these: 762s 131 (100.00%) were paired; of these: 762s 131 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 131 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 131 pairs aligned 0 times concordantly or discordantly; of these: 762s 262 mates make up the pairs; of these: 762s 242 (92.37%) aligned 0 times 762s 9 (3.44%) aligned exactly 1 time 762s 11 (4.20%) aligned >1 times 762s 7.63% overall alignment rate 762s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.2 762s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.1 762s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 3 762s Reference gaps introduced: 1 762s Read gaps introduced: 1 762s Rearrangements introduced: 1 762s Created read sampler 762s Sampling 115 reads 762s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 762s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s *** Run 84 of 100 762s /usr/bin/bowtie2 --trim5 0 -k 7 --score-min L,6.3997733164489,2.29961929305812 --np 4 --trim3 1 --ma 3.0138082449202 --cp-min 2 -D 14 --cp-ival 1 -q -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq 762s Parsed 58 reference bases 762s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '25' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '29' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Read 50 alignments... 762s Read 100 alignments... 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: skipping mate #1 of read '74' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '74' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 762s Warning: skipping mate #1 of read '91' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '91' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 762s Read 150 alignments... 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 762s Read 200 alignments... 762s 115 reads; of these: 762s 115 (100.00%) were paired; of these: 762s 115 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 115 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 115 pairs aligned 0 times concordantly or discordantly; of these: 762s 230 mates make up the pairs; of these: 762s 211 (91.74%) aligned 0 times 762s 7 (3.04%) aligned exactly 1 time 762s 12 (5.22%) aligned >1 times 762s 8.26% overall alignment rate 762s Read 250 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CTG 762s CTG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CC 762s CC 762s Processing line... 762s CC 762s CC 762s Processing line... 762s CC 762s CC 762s Processing line... 762s CC 762s CC 762s Processing line... 762s CC 762s CC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s ACGCG 762s ACGCG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CTATA 762s CTATA 762s Processing line... 762s TATAG 762s TATAG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CACT 762s CACT 762s Processing line... 762s CACT 762s CACT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s AT 762s AT 762s Processing line... 762s AT 762s AT 762s Processing line... 762s AT 762s AT 762s Processing line... 762s AT 762s AT 762s Processing line... 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s Processing line... 762s CGCG 762s CGCG 762s Processing line... 762s CGCG 762s CGCG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s ACA 762s ACA 762s Processing line... 762s ACA 762s ACA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CA 762s CA 762s Processing line... 762s CA 762s CA 762s Processing line... 762s CA 762s CA 762s Processing line... 762s CA 762s CA 762s Processing line... 762s TG 762s TG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s AACG 762s AACG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TC 762s TC 762s Processing line... 762s TC 762s TC 762s Processing line... 762s TC 762s TC 762s Processing line... 762s TC 762s TC 762s Processing line... 762s Processing line... 762s AACA 762s AACA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TAGCA 762s TAGCA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s AC 762s AC 762s Processing line... 762s AC 762s AC 762s Processing line... 762s AC 762s AC 762s Processing line... 762s AC 762s AC 762s Processing line... 762s AC 762s AC 762s Processing line... 762s Processing line... 762s AG 762s AG 762s Processing line... 762s AG 762s AG 762s Processing line... 762s AG 762s AG 762s Processing line... 762s CT 762s CT 762s Processing line... 762s CT 762s CT 762s Processing line... 762s CT 762s CT 762s Processing line... 762s CT 762s CT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TCCTATA 762s TCCTATA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GCAC 762s GCAC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 59 alignments, 0 edits 762s --------------- 762s PASSED 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.2 762s *** Run 85 of 100 762s /usr/bin/bowtie2 --mm --rfg 25.4610295054445,13.3527726326071 --score-min L,3.72153352123236,1.54288164067312 --trim3 5 --cp-ival 1 --local --cp-min 8 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 762s Introducing 8 SNPs, 0/0 ref/read gaps, and 2 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.1 762s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 11 762s Reference gaps introduced: 0 762s Read gaps introduced: 0 762s Rearrangements introduced: 2 762s Created read sampler 762s Sampling 86 reads 762s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 762s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s Parsed 58 reference bases 762s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '1' because it was < 2 characters long 762s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '8' because it was < 2 characters long 762s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '9' because it was < 2 characters long 762s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '17' because it was < 2 characters long 762s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '18' because it was < 2 characters long 762s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '19' because it was < 2 characters long 762s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '20' because it was < 2 characters long 762s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '21' because it was < 2 characters long 762s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '32' because it was < 2 characters long 762s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '48' because it was < 2 characters long 762s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '54' because it was < 2 characters long 762s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '56' because it was < 2 characters long 762s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '60' because it was < 2 characters long 762s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '61' because it was < 2 characters long 762s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '69' because it was < 2 characters long 762s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '72' because it was < 2 characters long 762s 86 reads; of these: 762s 86 (100.00%) were unpaired; of these: 762s 84 (97.67%) aligned 0 times 762s 2 (2.33%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 2.33% overall alignment rate 762s Read 50 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s /usr/bin/bowtie2 --mm --rfg 25.4610295054445,13.3527726326071 --score-min L,3.72153352123236,1.54288164067312 --trim3 5 --cp-ival 1 --local --cp-min 8 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CTCACTGCTCTCCTA 762s CTCACTGCTCTCCTA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CCTATAG 762s CCTATAG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 2 alignments, 0 edits 762s --------------- 762s PASSED 762s ALSO checking that bowtie2 and bowtie2-align match up 762s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '1' because it was < 2 characters long 762s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '8' because it was < 2 characters long 762s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '9' because it was < 2 characters long 762s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '17' because it was < 2 characters long 762s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '18' because it was < 2 characters long 762s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '19' because it was < 2 characters long 762s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '20' because it was < 2 characters long 762s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '21' because it was < 2 characters long 762s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '32' because it was < 2 characters long 762s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '48' because it was < 2 characters long 762s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '54' because it was < 2 characters long 762s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '56' because it was < 2 characters long 762s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '60' because it was < 2 characters long 762s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '61' because it was < 2 characters long 762s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '69' because it was < 2 characters long 762s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 762s Warning: skipping read '72' because it was < 2 characters long 762s 86 reads; of these: 762s 86 (100.00%) were unpaired; of these: 762s 84 (97.67%) aligned 0 times 762s 2 (2.33%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 2.33% overall alignment rate 762s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.1 762s Introducing 4 SNPs, 0/2 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.2 762s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 8 762s Reference gaps introduced: 0 762s Read gaps introduced: 2 762s Rearrangements introduced: 1 762s Created read sampler 762s Sampling 86 reads 762s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 762s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s *** Run 86 of 100 762s /usr/bin/bowtie2 --score-min L,5.85713910118529,7.23632047003472 --rfg 7.44492071346299,18.7436375511853 --rdg 37.6356075406199 --np 1 -i S,0.903574281280774 --trim5 5 -N 0 -L21 --cp-min 3 --cp-ival 3 -q -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq 762s Parsed 58 reference bases 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '8' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '10' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '12' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '16' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '17' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '25' because it was < 2 characters long 762s Warning: skipping mate #2 of read '25' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '26' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '39' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '42' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 762s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '50' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '59' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '62' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '76' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '78' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Read 50 alignments... 762s Read 100 alignments... 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s 86 reads; of these: 762s 79 (91.86%) were paired; of these: 762s 79 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 79 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 79 pairs aligned 0 times concordantly or discordantly; of these: 762s 158 mates make up the pairs; of these: 762s 155 (98.10%) aligned 0 times 762s 2 (1.27%) aligned exactly 1 time 762s 1 (0.63%) aligned >1 times 762s 7 (8.14%) were unpaired; of these: 762s 6 (85.71%) aligned 0 times 762s 1 (14.29%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 2.42% overall alignment rate 762s Read 150 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s AAA 762s AAA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TC 762s TC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s ATC 762s ATC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s /usr/bin/bowtie2 --score-min L,5.85713910118529,7.23632047003472 --rfg 7.44492071346299,18.7436375511853 --rdg 37.6356075406199 --np 1 -i S,0.903574281280774 --trim5 5 -N 0 -L21 --cp-min 3 --cp-ival 3 -q -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s AACGCG 762s AACGCG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 4 alignments, 0 edits 762s --------------- 762s PASSED 762s ALSO checking that bowtie2 and bowtie2-align match up 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '8' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '10' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '12' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '16' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '17' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '25' because it was < 2 characters long 762s Warning: skipping mate #2 of read '25' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '26' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '39' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '42' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 762s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '50' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '59' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '62' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '76' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '78' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s 86 reads; of these: 762s 79 (91.86%) were paired; of these: 762s 79 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 79 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 79 pairs aligned 0 times concordantly or discordantly; of these: 762s 158 mates make up the pairs; of these: 762s 155 (98.10%) aligned 0 times 762s 2 (1.27%) aligned exactly 1 time 762s 1 (0.63%) aligned >1 times 762s 7 (8.14%) were unpaired; of these: 762s 6 (85.71%) aligned 0 times 762s 1 (14.29%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 2.42% overall alignment rate 762s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 762s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 762s /usr/bin/bowtie2 --score-min L,5.85713910118529,7.23632047003472 --rfg 7.44492071346299,18.7436375511853 --rdg 37.6356075406199 --np 1 -i S,0.903574281280774 --trim5 5 -N 0 -L21 --cp-min 3 --cp-ival 3 -q -p 2 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '8' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '10' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '12' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '16' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '17' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '25' because it was < 2 characters long 762s Warning: skipping mate #2 of read '25' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '26' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '39' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '42' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 762s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '50' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '59' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '62' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '76' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '78' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s 86 reads; of these: 762s 79 (91.86%) were paired; of these: 762s 79 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 79 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 79 pairs aligned 0 times concordantly or discordantly; of these: 762s 158 mates make up the pairs; of these: 762s 155 (98.10%) aligned 0 times 762s 2 (1.27%) aligned exactly 1 time 762s 1 (0.63%) aligned >1 times 762s 7 (8.14%) were unpaired; of these: 762s 6 (85.71%) aligned 0 times 762s 1 (14.29%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 2.42% overall alignment rate 762s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 762s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 762s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 762s /usr/bin/bowtie2 --score-min L,5.85713910118529,7.23632047003472 --rfg 7.44492071346299,18.7436375511853 --rdg 37.6356075406199 --np 1 -i S,0.903574281280774 --trim5 5 -N 0 -L21 --cp-min 3 --cp-ival 3 -q -p 4 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.fastq -2 /tmp/Sim.pm.sD3XFvJi_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 762s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '8' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '10' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '12' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '16' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 762s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '17' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '25' because it was < 2 characters long 762s Warning: skipping mate #2 of read '25' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '26' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 762s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '39' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 762s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '42' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 762s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '50' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 762s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '59' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 762s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '62' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 762s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '76' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 762s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '78' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 762s 86 reads; of these: 762s 79 (91.86%) were paired; of these: 762s 79 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 79 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 79 pairs aligned 0 times concordantly or discordantly; of these: 762s 158 mates make up the pairs; of these: 762s 155 (98.10%) aligned 0 times 762s 2 (1.27%) aligned exactly 1 time 762s 1 (0.63%) aligned >1 times 762s 7 (8.14%) were unpaired; of these: 762s 6 (85.71%) aligned 0 times 762s 1 (14.29%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 2.42% overall alignment rate 762s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.1 762s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.2 762s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 0 762s Reference gaps introduced: 2 762s Read gaps introduced: 0 762s Rearrangements introduced: 1 762s Created read sampler 762s Sampling 32 reads 762s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 762s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s *** Run 87 of 100 762s /usr/bin/bowtie2 --mm --score-min L,3.38771669145483,2.64748191322943 --rfg 48.7091258141565,19.3156277410818 --trim3 9 -N 1 --cp-ival 1 -i C --trim5 5 --np 4 --ma 31.8812634562642 --cp-min 6 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq 762s Parsed 58 reference bases 762s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 762s 32 reads; of these: 762s 32 (100.00%) were unpaired; of these: 762s 27 (84.38%) aligned 0 times 762s 3 (9.38%) aligned exactly 1 time 762s 2 (6.25%) aligned >1 times 762s 15.62% overall alignment rate 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s AGC 762s AGC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CCTTACAACAACG 762s CCTTACAACAACG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CCTATA 762s CCTATA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CA 762s CA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GCCTTACAAC 762s GCCTTACAAC 762s --- Summary --- 762s Read 1 reference strings 762s Checked 5 alignments, 0 edits 762s --------------- 762s PASSED 762s ALSO checking that bowtie2 and bowtie2-align match up 762s /usr/bin/bowtie2 --mm --score-min L,3.38771669145483,2.64748191322943 --rfg 48.7091258141565,19.3156277410818 --trim3 9 -N 1 --cp-ival 1 -i C --trim5 5 --np 4 --ma 31.8812634562642 --cp-min 6 --qseq -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 762s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 762s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (1) 762s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 762s 32 reads; of these: 762s 32 (100.00%) were unpaired; of these: 762s 27 (84.38%) aligned 0 times 762s 3 (9.38%) aligned exactly 1 time 762s 2 (6.25%) aligned >1 times 762s 15.62% overall alignment rate 762s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.2 762s Introducing 4 SNPs, 2/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.1 762s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 6 762s Reference gaps introduced: 3 762s Read gaps introduced: 0 762s Rearrangements introduced: 0 762s Created read sampler 762s Sampling 105 reads 762s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 762s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s Parsed 58 reference bases 762s *** Run 88 of 100 762s /usr/bin/bowtie2 --rdg 42.5255793531771,13.4780037811167 --score-min L,9.44847886316511,1.5894867089141 --cp-ival 1 -D 41 --mp 6.4697586400106,2.69580522977907 -k 6 -i L --np 1 -R 3 --cp-min 5 --ma 32.1616409154327 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 762s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 762s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 762s Warning: skipping read '37' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '37' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 762s Warning: skipping read '51' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '51' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 762s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '60' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 762s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '66' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 762s 105 reads; of these: 762s 105 (100.00%) were unpaired; of these: 762s 95 (90.48%) aligned 0 times 762s 4 (3.81%) aligned exactly 1 time 762s 6 (5.71%) aligned >1 times 762s 9.52% overall alignment rate 762s Read 50 alignments... 762s Read 100 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TCT 762s TCT 762s Processing line... 762s TCT 762s TCT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GCTC 762s GCTC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CC 762s CC 762s Processing line... 762s CC 762s CC 762s Processing line... 762s CC 762s CC 762s Processing line... 762s CC 762s CC 762s Processing line... 762s CC 762s CC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TACAACAACGC 762s TACAACAACGC 762s Processing line... 762s Processing line... 762s TA 762s TA 762s Processing line... 762s TA 762s TA 762s Processing line... 762s TA 762s TA 762s Processing line... 762s TA 762s TA 762s Processing line... 762s TA 762s TA 762s Processing line... 762s TA 762s TA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s GCACT 762s GCACT 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CAAC 762s CAAC 762s Processing line... 762s CAAC 762s CAAC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s GC 762s GC 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s CAA 762s CAA 762s Processing line... 762s CAA 762s CAA 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s TTACAACAACG 762s TTACAACAACG 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 27 alignments, 0 edits 762s --------------- 762s PASSED 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.2 762s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.1 762s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 3 762s Reference gaps introduced: 0 762s Read gaps introduced: 0 762s Rearrangements introduced: 3 762s Created read sampler 762s Sampling 30 reads 762s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 762s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 762s *** Run 89 of 100 762s /usr/bin/bowtie2 --mm --score-min L,3.67523027695463,4.90034372663555 --gbar 2 --trim3 8 --mp 7.03195398427364,4.29240483970121 --cp-ival 1 --n-ceil 1.25828239994776,0.328342399750419 -k 6 --np 2 -R 3 --cp-min 6 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 762s parsing sequence Sim.pm.1... 762s parsing sequence Sim.pm.2... 762s Parsed 58 reference bases 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 762s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 762s Warning: skipping read '3' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 762s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '4' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 762s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '16' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 762s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '23' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 762s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '25' because it was < 2 characters long 762s Warning: skipping mate #2 of read '25' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 762s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '27' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 762s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 762s Warning: skipping mate #1 of read '28' because it was < 2 characters long 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 762s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 762s 30 reads; of these: 762s 26 (86.67%) were paired; of these: 762s 26 (100.00%) aligned concordantly 0 times 762s 0 (0.00%) aligned concordantly exactly 1 time 762s 0 (0.00%) aligned concordantly >1 times 762s ---- 762s 26 pairs aligned concordantly 0 times; of these: 762s 0 (0.00%) aligned discordantly 1 time 762s ---- 762s 26 pairs aligned 0 times concordantly or discordantly; of these: 762s 52 mates make up the pairs; of these: 762s 52 (100.00%) aligned 0 times 762s 0 (0.00%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 4 (13.33%) were unpaired; of these: 762s 4 (100.00%) aligned 0 times 762s 0 (0.00%) aligned exactly 1 time 762s 0 (0.00%) aligned >1 times 762s 0.00% overall alignment rate 762s Read 50 alignments... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s Processing line... 762s --- Summary --- 762s Read 1 reference strings 762s Checked 0 alignments, 0 edits 762s --------------- 762s PASSED 762s Flattened IUPAC characters 762s Mutating sequence Sim.pm.2 762s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutating sequence Sim.pm.1 762s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 762s Finished SNPs 762s Finished ref gaps 762s Finished read gaps 762s Mutated reference genome to subject genome 762s SNPs introduced: 2 762s Reference gaps introduced: 0 762s Read gaps introduced: 1 762s Rearrangements introduced: 0 762s Created read sampler 762s Sampling 50 reads 762s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 762s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 762s parsing sequence Sim.pm.1... 762s *** Run 90 of 100 762s /usr/bin/bowtie2 --mm --score-min L,5.00397868796167,9.23217125364326 --trim3 5 --cp-ival 1 -D 18 --local --trim5 6 -R 4 --cp-min 6 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 762s parsing sequence Sim.pm.2... 762s Parsed 58 reference bases 763s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '2' because it was < 2 characters long 763s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '3' because it was < 2 characters long 763s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '4' because it was < 2 characters long 763s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '7' because it was < 2 characters long 763s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '11' because it was < 2 characters long 763s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '12' because it was < 2 characters long 763s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '13' because it was < 2 characters long 763s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '14' because it was < 2 characters long 763s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '15' because it was < 2 characters long 763s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '17' because it was < 2 characters long 763s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '24' because it was < 2 characters long 763s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '25' because it was < 2 characters long 763s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '26' because it was < 2 characters long 763s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '29' because it was < 2 characters long 763s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '30' because it was < 2 characters long 763s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '34' because it was < 2 characters long 763s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '35' because it was < 2 characters long 763s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '37' because it was < 2 characters long 763s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '38' because it was < 2 characters long 763s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '39' because it was < 2 characters long 763s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '40' because it was < 2 characters long 763s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '43' because it was < 2 characters long 763s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '46' because it was < 2 characters long 763s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '48' because it was < 2 characters long 763s 50 reads; of these: 763s 50 (100.00%) were unpaired; of these: 763s 50 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s Read 50 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s /usr/bin/bowtie2 --mm --score-min L,5.00397868796167,9.23217125364326 --trim3 5 --cp-ival 1 -D 18 --local --trim5 6 -R 4 --cp-min 6 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 0 alignments, 0 edits 763s --------------- 763s PASSED 763s ALSO checking that bowtie2 and bowtie2-align match up 763s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '2' because it was < 2 characters long 763s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '3' because it was < 2 characters long 763s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '4' because it was < 2 characters long 763s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '7' because it was < 2 characters long 763s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '11' because it was < 2 characters long 763s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '12' because it was < 2 characters long 763s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '13' because it was < 2 characters long 763s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '14' because it was < 2 characters long 763s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '15' because it was < 2 characters long 763s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '17' because it was < 2 characters long 763s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '24' because it was < 2 characters long 763s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '25' because it was < 2 characters long 763s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '26' because it was < 2 characters long 763s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '29' because it was < 2 characters long 763s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '30' because it was < 2 characters long 763s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '34' because it was < 2 characters long 763s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '35' because it was < 2 characters long 763s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '37' because it was < 2 characters long 763s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '38' because it was < 2 characters long 763s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '39' because it was < 2 characters long 763s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '40' because it was < 2 characters long 763s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '43' because it was < 2 characters long 763s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '46' because it was < 2 characters long 763s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '48' because it was < 2 characters long 763s 50 reads; of these: 763s 50 (100.00%) were unpaired; of these: 763s 50 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.2 763s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.1 763s Introducing 3 SNPs, 0/3 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 7 763s Reference gaps introduced: 1 763s Read gaps introduced: 3 763s Rearrangements introduced: 0 763s Created read sampler 763s Sampling 53 reads 763s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 763s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s *** Run 91 of 100 763s /usr/bin/bowtie2 --cp-min 2 --np 5 --trim3 8 --local --cp-ival 1 -D 46 --mp 7.78369318070539,3.53177213352203 --gbar 2 --score-min L,5.95220409004826,5.95553976074834 --rfg 42.0470923450789 --rdg 27.8105898908806 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 763s Parsed 58 reference bases 763s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '2' because it was < 2 characters long 763s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '3' because it was < 2 characters long 763s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '5' because it was < 2 characters long 763s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '6' because it was < 2 characters long 763s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '7' because it was < 2 characters long 763s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '12' because it was < 2 characters long 763s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '15' because it was < 2 characters long 763s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '18' because it was < 2 characters long 763s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '19' because it was < 2 characters long 763s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '21' because it was < 2 characters long 763s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '24' because it was < 2 characters long 763s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '27' because it was < 2 characters long 763s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '29' because it was < 2 characters long 763s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '30' because it was < 2 characters long 763s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '32' because it was < 2 characters long 763s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '33' because it was < 2 characters long 763s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '34' because it was < 2 characters long 763s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '41' because it was < 2 characters long 763s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '42' because it was < 2 characters long 763s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '43' because it was < 2 characters long 763s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '47' because it was < 2 characters long 763s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '52' because it was < 2 characters long 763s 53 reads; of these: 763s 53 (100.00%) were unpaired; of these: 763s 53 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s Read 50 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 0 alignments, 0 edits 763s --------------- 763s PASSED 763s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 763s /usr/bin/bowtie2 --cp-min 2 --np 5 --trim3 8 --local --cp-ival 1 -D 46 --mp 7.78369318070539,3.53177213352203 --gbar 2 --score-min L,5.95220409004826,5.95553976074834 --rfg 42.0470923450789 --rdg 27.8105898908806 -f -p 2 -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 763s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '2' because it was < 2 characters long 763s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '3' because it was < 2 characters long 763s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '5' because it was < 2 characters long 763s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '6' because it was < 2 characters long 763s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '7' because it was < 2 characters long 763s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '12' because it was < 2 characters long 763s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '15' because it was < 2 characters long 763s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '18' because it was < 2 characters long 763s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '19' because it was < 2 characters long 763s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '21' because it was < 2 characters long 763s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '24' because it was < 2 characters long 763s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '27' because it was < 2 characters long 763s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '29' because it was < 2 characters long 763s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '30' because it was < 2 characters long 763s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '32' because it was < 2 characters long 763s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '33' because it was < 2 characters long 763s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '34' because it was < 2 characters long 763s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '41' because it was < 2 characters long 763s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '42' because it was < 2 characters long 763s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '43' because it was < 2 characters long 763s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '47' because it was < 2 characters long 763s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '52' because it was < 2 characters long 763s 53 reads; of these: 763s 53 (100.00%) were unpaired; of these: 763s 53 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 763s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.1 763s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 763s Finished SNPs 763s *** Run 92 of 100 763s /usr/bin/bowtie2 --cp-min 2 --n-ceil 0.172439679809554,1.04997363954213 --cp-ival 2 --local --nofw -N 1 --np 2 --score-min L,4.63713707037114,9.45234886344972 --rdg 21.161944533589,10.1795183272376 -M 4 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.2 763s Introducing 3 SNPs, 0/2 ref/read gaps, and 3 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 6 763s Reference gaps introduced: 0 763s Read gaps introduced: 2 763s Rearrangements introduced: 4 763s Created read sampler 763s Sampling 15 reads 763s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 763s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s Parsed 58 reference bases 763s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 763s 15 reads; of these: 763s 15 (100.00%) were unpaired; of these: 763s 15 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 0 alignments, 0 edits 763s --------------- 763s PASSED 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.2 763s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.1 763s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 8 763s Reference gaps introduced: 0 763s Read gaps introduced: 0 763s Rearrangements introduced: 0 763s Created read sampler 763s Sampling 92 reads 763s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 763s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s Parsed 58 reference bases 763s *** Run 93 of 100 763s /usr/bin/bowtie2 -k 6 --trim5 2 --np 5 --cp-min 6 --mm --score-min L,1.13120454230923,6.91824889930485 --rdg 47.0034035236059 --rfg 32.5882691582678,5.524658392461 --trim3 8 --cp-ival 2 -D 29 --local -N 0 -L26 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 763s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 763s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 763s Read 50 alignments... 763s 92 reads; of these: 763s 71 (77.17%) were paired; of these: 763s 71 (100.00%) aligned concordantly 0 times 763s 0 (0.00%) aligned concordantly exactly 1 time 763s 0 (0.00%) aligned concordantly >1 times 763s ---- 763s 71 pairs aligned concordantly 0 times; of these: 763s 0 (0.00%) aligned discordantly 1 time 763s ---- 763s 71 pairs aligned 0 times concordantly or discordantly; of these: 763s 142 mates make up the pairs; of these: 763s 142 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 21 (22.83%) were unpaired; of these: 763s 21 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s Read 100 alignments... 763s Read 150 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s /usr/bin/bowtie2 -k 6 --trim5 2 --np 5 --cp-min 6 --mm --score-min L,1.13120454230923,6.91824889930485 --rdg 47.0034035236059 --rfg 32.5882691582678,5.524658392461 --trim3 8 --cp-ival 2 -D 29 --local -N 0 -L26 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 0 alignments, 0 edits 763s --------------- 763s PASSED 763s ALSO checking that bowtie2 and bowtie2-align match up 763s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 763s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 763s 92 reads; of these: 763s 71 (77.17%) were paired; of these: 763s 71 (100.00%) aligned concordantly 0 times 763s 0 (0.00%) aligned concordantly exactly 1 time 763s 0 (0.00%) aligned concordantly >1 times 763s ---- 763s 71 pairs aligned concordantly 0 times; of these: 763s 0 (0.00%) aligned discordantly 1 time 763s ---- 763s 71 pairs aligned 0 times concordantly or discordantly; of these: 763s 142 mates make up the pairs; of these: 763s 142 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 21 (22.83%) were unpaired; of these: 763s 21 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 763s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 763s /usr/bin/bowtie2 -k 6 --trim5 2 --np 5 --cp-min 6 --mm --score-min L,1.13120454230923,6.91824889930485 --rdg 47.0034035236059 --rfg 32.5882691582678,5.524658392461 --trim3 8 --cp-ival 2 -D 29 --local -N 0 -L26 --qseq -p 3 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 763s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 763s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 763s 92 reads; of these: 763s 71 (77.17%) were paired; of these: 763s 71 (100.00%) aligned concordantly 0 times 763s 0 (0.00%) aligned concordantly exactly 1 time 763s 0 (0.00%) aligned concordantly >1 times 763s ---- 763s 71 pairs aligned concordantly 0 times; of these: 763s 0 (0.00%) aligned discordantly 1 time 763s ---- 763s 71 pairs aligned 0 times concordantly or discordantly; of these: 763s 142 mates make up the pairs; of these: 763s 142 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 21 (22.83%) were unpaired; of these: 763s 21 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 763s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 763s /usr/bin/bowtie2 -k 6 --trim5 2 --np 5 --cp-min 6 --mm --score-min L,1.13120454230923,6.91824889930485 --rdg 47.0034035236059 --rfg 32.5882691582678,5.524658392461 --trim3 8 --cp-ival 2 -D 29 --local -N 0 -L26 --qseq -p 3 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 763s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 763s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 763s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 763s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 763s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 763s 92 reads; of these: 763s 71 (77.17%) were paired; of these: 763s 71 (100.00%) aligned concordantly 0 times 763s 0 (0.00%) aligned concordantly exactly 1 time 763s 0 (0.00%) aligned concordantly >1 times 763s ---- 763s 71 pairs aligned concordantly 0 times; of these: 763s 0 (0.00%) aligned discordantly 1 time 763s ---- 763s 71 pairs aligned 0 times concordantly or discordantly; of these: 763s 142 mates make up the pairs; of these: 763s 142 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 21 (22.83%) were unpaired; of these: 763s 21 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.2 763s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.1 763s Introducing 9 SNPs, 1/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 13 763s Reference gaps introduced: 1 763s Read gaps introduced: 0 763s Rearrangements introduced: 0 763s Created read sampler 763s Sampling 21 reads 763s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 763s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s *** Run 94 of 100 763s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 0.545089728121006,0.908629431730836 --cp-min 14 --mp 2.88119505248106,1.6635044405227 --nofw --np 2 --score-min L,3.12897435853389,4.81682605456105 -M 6 -i L,0.14050186306362 -r -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.raw 763s Parsed 58 reference bases 763s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 763s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 763s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '13' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 763s 21 reads; of these: 763s 21 (100.00%) were unpaired; of these: 763s 20 (95.24%) aligned 0 times 763s 1 (4.76%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 4.76% overall alignment rate 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CCTTACAACAA 763s CCTTACAACAA 763s --- Summary --- 763s Read 1 reference strings 763s Checked 1 alignments, 0 edits 763s --------------- 763s PASSED 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.1 763s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.2 763s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 13 763s Reference gaps introduced: 1 763s Read gaps introduced: 0 763s Rearrangements introduced: 0 763s Created read sampler 763s Sampling 127 reads 763s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fastq & /tmp/Sim.pm.sD3XFvJi_2.fastq 763s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s *** Run 95 of 100 763s /usr/bin/bowtie2 --local --cp-ival 1 -D 30 --mp 7.15875438111561,6.30835571289539 -N 0 --trim3 1 --gbar 2 --rdg 36.6455452995707 --score-min L,9.57036058301136,4.9764256696199 -a --cp-min 2 -R 2 --np 4 --trim5 9 -q -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fastq 763s Parsed 58 reference bases 763s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '3' because it was < 2 characters long 763s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '6' because it was < 2 characters long 763s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '9' because it was < 2 characters long 763s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '10' because it was < 2 characters long 763s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '11' because it was < 2 characters long 763s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '16' because it was < 2 characters long 763s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '22' because it was < 2 characters long 763s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '27' because it was < 2 characters long 763s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '31' because it was < 2 characters long 763s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '33' because it was < 2 characters long 763s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '34' because it was < 2 characters long 763s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '35' because it was < 2 characters long 763s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '37' because it was < 2 characters long 763s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '40' because it was < 2 characters long 763s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '41' because it was < 2 characters long 763s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '42' because it was < 2 characters long 763s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '43' because it was < 2 characters long 763s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '47' because it was < 2 characters long 763s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '49' because it was < 2 characters long 763s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '50' because it was < 2 characters long 763s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '51' because it was < 2 characters long 763s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '54' because it was < 2 characters long 763s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '55' because it was < 2 characters long 763s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '56' because it was < 2 characters long 763s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '57' because it was < 2 characters long 763s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '59' because it was < 2 characters long 763s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '61' because it was < 2 characters long 763s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '64' because it was < 2 characters long 763s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '67' because it was < 2 characters long 763s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '71' because it was < 2 characters long 763s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '73' because it was < 2 characters long 763s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '76' because it was < 2 characters long 763s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '85' because it was < 2 characters long 763s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '88' because it was < 2 characters long 763s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '95' because it was < 2 characters long 763s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '96' because it was < 2 characters long 763s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '97' because it was < 2 characters long 763s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '102' because it was < 2 characters long 763s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '106' because it was < 2 characters long 763s Warning: skipping read '107' because length (1) <= # seed mismatches (0) 763s Warning: skipping read '107' because it was < 2 characters long 763s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '108' because it was < 2 characters long 763s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '112' because it was < 2 characters long 763s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '113' because it was < 2 characters long 763s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '118' because it was < 2 characters long 763s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '119' because it was < 2 characters long 763s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '121' because it was < 2 characters long 763s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 763s Warning: skipping read '124' because it was < 2 characters long 763s 127 reads; of these: 763s 127 (100.00%) were unpaired; of these: 763s 127 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s Read 50 alignments... 763s Read 100 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s *** Run 96 of 100 763s /usr/bin/bowtie2 -a --score-min L,3.08308592627864,6.50491298871003 --rfg 29.1623817993339,16.9000210582753 --nofw -N 0 --local --cp-ival 1 -D 22 --np 3 --cp-min 4 -f -x /tmp/Sim.pm.sD3XFvJi /tmp/Sim.pm.sD3XFvJi_1.fasta 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 0 alignments, 0 edits 763s --------------- 763s PASSED 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.1 763s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.2 763s Introducing 0 SNPs, 1/2 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 1 763s Reference gaps introduced: 2 763s Read gaps introduced: 2 763s Rearrangements introduced: 0 763s Created read sampler 763s Sampling 37 reads 763s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 763s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s Parsed 58 reference bases 763s 37 reads; of these: 763s 37 (100.00%) were unpaired; of these: 763s 37 (100.00%) aligned 0 times 763s 0 (0.00%) aligned exactly 1 time 763s 0 (0.00%) aligned >1 times 763s 0.00% overall alignment rate 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 0 alignments, 0 edits 763s --------------- 763s PASSED 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.1 763s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.2 763s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 1 763s Reference gaps introduced: 0 763s Read gaps introduced: 1 763s Rearrangements introduced: 2 763s Created read sampler 763s Sampling 141 reads 763s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.qseq & /tmp/Sim.pm.sD3XFvJi_2.qseq 763s *** Run 97 of 100 763s /usr/bin/bowtie2 --score-min L,8.56833167528184,3.20205909627258 --rfg 48.3838520607108 --rdg 25.4802108876491 --mm --cp-min 4 --cp-ival 1 -R 4 --qseq -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq 763s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 763s parsing sequence Sim.pm.1... 763s parsing sequence Sim.pm.2... 763s Parsed 58 reference bases 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 763s Read 50 alignments... 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 763s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 763s Warning: skipping mate #2 of read 'R_1_1_1_111_111_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 763s Read 100 alignments... 763s Read 150 alignments... 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 763s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_139_139_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_139_139_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 763s Warning: skipping mate #2 of read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 763s Warning: skipping mate #2 of read 'R_1_1_1_141_141_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 763s Read 200 alignments... 763s 141 reads; of these: 763s 141 (100.00%) were paired; of these: 763s 141 (100.00%) aligned concordantly 0 times 763s 0 (0.00%) aligned concordantly exactly 1 time 763s 0 (0.00%) aligned concordantly >1 times 763s ---- 763s 141 pairs aligned concordantly 0 times; of these: 763s 0 (0.00%) aligned discordantly 1 time 763s ---- 763s 141 pairs aligned 0 times concordantly or discordantly; of these: 763s 282 mates make up the pairs; of these: 763s 259 (91.84%) aligned 0 times 763s 19 (6.74%) aligned exactly 1 time 763s 4 (1.42%) aligned >1 times 763s 8.16% overall alignment rate 763s Read 250 alignments... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CTCT 763s CTCT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CTTACAACAACGC 763s CTTACAACAACGC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CTATAG 763s CTATAG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s TAC 763s TAC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s ACAACAACGC 763s ACAACAACGC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s /usr/bin/bowtie2 --score-min L,8.56833167528184,3.20205909627258 --rfg 48.3838520607108 --rdg 25.4802108876491 --mm --cp-min 4 --cp-ival 1 -R 4 --qseq -p 3 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.qseq -2 /tmp/Sim.pm.sD3XFvJi_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s ACG 763s ACG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s ACTG 763s ACTG 763s Processing line... 763s Processing line... 763s CTTACAACAACG 763s CTTACAACAACG 763s Processing line... 763s ACT 763s ACT 763s Processing line... 763s Processing line... 763s Processing line... 763s ACGC 763s ACGC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s AA 763s AA 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CTTACAACAA 763s CTTACAACAA 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CTCC 763s CTCC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s TACAAC 763s TACAAC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s TACAACA 763s TACAACA 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s ACAACG 763s ACAACG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s TCACTGCTCTC 763s TCACTGCTCTC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CCTTACAACA 763s CCTTACAACA 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CCTTACAACAACG 763s CCTTACAACAACG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CGC 763s CGC 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s CCTT 763s CCTT 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s ACAACG 763s ACAACG 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s Processing line... 763s GCCTTACAACA 763s GCCTTACAACA 763s Processing line... 763s Processing line... 763s Processing line... 763s --- Summary --- 763s Read 1 reference strings 763s Checked 23 alignments, 0 edits 763s --------------- 763s PASSED 763s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 763s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 763s Warning: skipping mate #2 of read 'R_1_1_1_111_111_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 763s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 763s Warning: skipping mate #1 of read 'R_1_1_1_139_139_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_139_139_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #1 of read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 763s Warning: skipping mate #2 of read 'R_1_1_1_139_139_1/1' because it was < 2 characters long 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 763s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 763s Warning: skipping mate #2 of read 'R_1_1_1_141_141_1/1' because length (1) <= # seed mismatches (0) 763s Warning: skipping mate #2 of read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 763s 141 reads; of these: 763s 141 (100.00%) were paired; of these: 763s 141 (100.00%) aligned concordantly 0 times 763s 0 (0.00%) aligned concordantly exactly 1 time 763s 0 (0.00%) aligned concordantly >1 times 763s ---- 763s 141 pairs aligned concordantly 0 times; of these: 763s 0 (0.00%) aligned discordantly 1 time 763s ---- 763s 141 pairs aligned 0 times concordantly or discordantly; of these: 763s 282 mates make up the pairs; of these: 763s 259 (91.84%) aligned 0 times 763s 19 (6.74%) aligned exactly 1 time 763s 4 (1.42%) aligned >1 times 763s 8.16% overall alignment rate 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 763s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 763s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 763s Flattened IUPAC characters 763s Mutating sequence Sim.pm.1 763s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutating sequence Sim.pm.2 763s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 763s Finished SNPs 763s Finished ref gaps 763s Finished read gaps 763s Mutated reference genome to subject genome 763s SNPs introduced: 5 763s Reference gaps introduced: 1 763s Read gaps introduced: 2 763s Rearrangements introduced: 0 763s Created read sampler 763s Sampling 152 reads 764s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 764s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 764s parsing sequence Sim.pm.1... 764s *** Run 98 of 100 764s /usr/bin/bowtie2 -R 4 --cp-min 5 -M 2 --trim3 7 --mp 9.95863452250321,6.06493014354215 --nofw --local --cp-ival 1 --mm --rdg 13.6523965389718,13.2163875714843 --rfg 16.4161481845065,16.935148659855 --score-min L,2.62284717193898,5.38008585865949 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 764s parsing sequence Sim.pm.2... 764s Parsed 58 reference bases 764s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 764s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '5' because it was < 2 characters long 764s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '8' because it was < 2 characters long 764s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '10' because it was < 2 characters long 764s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '13' because it was < 2 characters long 764s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '17' because it was < 2 characters long 764s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '18' because it was < 2 characters long 764s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '23' because it was < 2 characters long 764s Warning: skipping mate #2 of read '23' because it was < 2 characters long 764s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '25' because it was < 2 characters long 764s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '39' because it was < 2 characters long 764s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '40' because it was < 2 characters long 764s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '41' because it was < 2 characters long 764s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '44' because it was < 2 characters long 764s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '49' because it was < 2 characters long 764s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '52' because it was < 2 characters long 764s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '53' because it was < 2 characters long 764s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '61' because it was < 2 characters long 764s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '66' because it was < 2 characters long 764s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '75' because it was < 2 characters long 764s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '82' because it was < 2 characters long 764s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '84' because it was < 2 characters long 764s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '98' because it was < 2 characters long 764s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '104' because it was < 2 characters long 764s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '113' because it was < 2 characters long 764s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '118' because it was < 2 characters long 764s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '122' because it was < 2 characters long 764s Warning: skipping mate #2 of read '128' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '128' because it was < 2 characters long 764s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '132' because it was < 2 characters long 764s Warning: skipping mate #2 of read '137' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '137' because it was < 2 characters long 764s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '138' because it was < 2 characters long 764s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '147' because it was < 2 characters long 764s Read 50 alignments... 764s Read 100 alignments... 764s 152 reads; of these: 764s 128 (84.21%) were paired; of these: 764s 128 (100.00%) aligned concordantly 0 times 764s 0 (0.00%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 128 pairs aligned concordantly 0 times; of these: 764s 0 (0.00%) aligned discordantly 1 time 764s ---- 764s 128 pairs aligned 0 times concordantly or discordantly; of these: 764s 256 mates make up the pairs; of these: 764s 256 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 24 (15.79%) were unpaired; of these: 764s 24 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s Read 150 alignments... 764s Read 200 alignments... 764s Read 250 alignments... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s /usr/bin/bowtie2 -R 4 --cp-min 5 -M 2 --trim3 7 --mp 9.95863452250321,6.06493014354215 --nofw --local --cp-ival 1 --mm --rdg 13.6523965389718,13.2163875714843 --rfg 16.4161481845065,16.935148659855 --score-min L,2.62284717193898,5.38008585865949 -r -p 4 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing 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Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing 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Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s --- Summary --- 764s Read 1 reference strings 764s Checked 0 alignments, 0 edits 764s --------------- 764s PASSED 764s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 764s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 764s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '5' because it was < 2 characters long 764s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '8' because it was < 2 characters long 764s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '10' because it was < 2 characters long 764s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '13' because it was < 2 characters long 764s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '17' because it was < 2 characters long 764s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '18' because it was < 2 characters long 764s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '23' because it was < 2 characters long 764s Warning: skipping mate #2 of read '23' because it was < 2 characters long 764s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '25' because it was < 2 characters long 764s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '39' because it was < 2 characters long 764s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '40' because it was < 2 characters long 764s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '41' because it was < 2 characters long 764s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '44' because it was < 2 characters long 764s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '49' because it was < 2 characters long 764s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '52' because it was < 2 characters long 764s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '53' because it was < 2 characters long 764s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '61' because it was < 2 characters long 764s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '66' because it was < 2 characters long 764s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '75' because it was < 2 characters long 764s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '82' because it was < 2 characters long 764s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '84' because it was < 2 characters long 764s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '98' because it was < 2 characters long 764s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '104' because it was < 2 characters long 764s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '113' because it was < 2 characters long 764s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '118' because it was < 2 characters long 764s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 764s Warning: skipping read '122' because it was < 2 characters long 764s Warning: skipping mate #2 of read '128' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '128' because it was < 2 characters long 764s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '132' because it was < 2 characters long 764s Warning: skipping mate #2 of read '137' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '137' because it was < 2 characters long 764s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '138' because it was < 2 characters long 764s Warning: skipping mate #1 of read '147' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '147' because it was < 2 characters long 764s 152 reads; of these: 764s 128 (84.21%) were paired; of these: 764s 128 (100.00%) aligned concordantly 0 times 764s 0 (0.00%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 128 pairs aligned concordantly 0 times; of these: 764s 0 (0.00%) aligned discordantly 1 time 764s ---- 764s 128 pairs aligned 0 times concordantly or discordantly; of these: 764s 256 mates make up the pairs; of these: 764s 256 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 24 (15.79%) were unpaired; of these: 764s 24 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 764s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 764s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 764s Flattened IUPAC characters 764s Mutating sequence Sim.pm.1 764s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutating sequence Sim.pm.2 764s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutated reference genome to subject genome 764s SNPs introduced: 8 764s Reference gaps introduced: 0 764s Read gaps introduced: 0 764s Rearrangements introduced: 0 764s Created read sampler 764s Sampling 40 reads 764s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.fasta & /tmp/Sim.pm.sD3XFvJi_2.fasta 764s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 764s parsing sequence Sim.pm.1... 764s parsing sequence Sim.pm.2... 764s Parsed 58 reference bases 764s *** Run 99 of 100 764s /usr/bin/bowtie2 --trim3 9 --mp 9.95134287833429,4.24268447776706 --nofw --cp-ival 2 -D 28 --mm --rdg 7.49982192017365 --score-min L,8.68761313587759,2.78498868305424 --ma 2.82946172473219 --cp-min 5 -i S,2.59361865253075,6.01441740860487 --trim5 4 -M 2 --norc --np 1 -f -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta 764s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 764s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '2' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 764s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '5' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 764s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '10' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 764s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '11' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 764s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '14' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 764s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '18' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 764s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '31' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 764s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '39' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 764s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '40' because it was < 2 characters long 764s 40 reads; of these: 764s 31 (77.50%) were paired; of these: 764s 31 (100.00%) aligned concordantly 0 times 764s 0 (0.00%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 31 pairs aligned concordantly 0 times; of these: 764s 0 (0.00%) aligned discordantly 1 time 764s ---- 764s 31 pairs aligned 0 times concordantly or discordantly; of these: 764s 62 mates make up the pairs; of these: 764s 62 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 9 (22.50%) were unpaired; of these: 764s 9 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s Read 50 alignments... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s /usr/bin/bowtie2 --trim3 9 --mp 9.95134287833429,4.24268447776706 --nofw --cp-ival 2 -D 28 --mm --rdg 7.49982192017365 --score-min L,8.68761313587759,2.78498868305424 --ma 2.82946172473219 --cp-min 5 -i S,2.59361865253075,6.01441740860487 --trim5 4 -M 2 --norc --np 1 -f -p 2 -x /tmp/Sim.pm.sD3XFvJi --reorder -1 /tmp/Sim.pm.sD3XFvJi_1.fasta -2 /tmp/Sim.pm.sD3XFvJi_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.reord.als 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s --- Summary --- 764s Read 1 reference strings 764s Checked 0 alignments, 0 edits 764s --------------- 764s PASSED 764s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 764s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 764s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '2' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 764s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '5' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 764s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '10' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 764s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #2 of read '11' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 764s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '14' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 764s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '18' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 764s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '31' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 764s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '39' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 764s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '40' because it was < 2 characters long 764s 40 reads; of these: 764s 31 (77.50%) were paired; of these: 764s 31 (100.00%) aligned concordantly 0 times 764s 0 (0.00%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 31 pairs aligned concordantly 0 times; of these: 764s 0 (0.00%) aligned discordantly 1 time 764s ---- 764s 31 pairs aligned 0 times concordantly or discordantly; of these: 764s 62 mates make up the pairs; of these: 764s 62 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 9 (22.50%) were unpaired; of these: 764s 9 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als /tmp/Sim.pm.sD3XFvJi.px.reord.als 764s Flattened IUPAC characters 764s Mutating sequence Sim.pm.2 764s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutating sequence Sim.pm.1 764s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutated reference genome to subject genome 764s *** Run 100 of 100 764s /usr/bin/bowtie2 --cp-min 5 -M 6 --trim5 6 --trim3 4 --cp-ival 3 --local -N 1 -L22 --rfg 36.2416213692808 --rdg 8.6348512288939 --score-min L,7.02637021580779,1.46973476369281 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw 764s SNPs introduced: 5 764s Reference gaps introduced: 1 764s Read gaps introduced: 0 764s Rearrangements introduced: 1 764s Created read sampler 764s Sampling 7 reads 764s Dumping reads to temporary files /tmp/Sim.pm.sD3XFvJi_1.raw & /tmp/Sim.pm.sD3XFvJi_2.raw 764s Parsing FASTA file /tmp/Sim.pm.sD3XFvJi.fa... 764s parsing sequence Sim.pm.1... 764s parsing sequence Sim.pm.2... 764s Parsed 58 reference bases 764s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 764s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '1' because it was < 2 characters long 764s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '3' because it was < 2 characters long 764s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '5' because it was < 2 characters long 764s 7 reads; of these: 764s 6 (85.71%) were paired; of these: 764s 6 (100.00%) aligned concordantly 0 times 764s 0 (0.00%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 6 pairs aligned concordantly 0 times; of these: 764s 0 (0.00%) aligned discordantly 1 time 764s ---- 764s 6 pairs aligned 0 times concordantly or discordantly; of these: 764s 12 mates make up the pairs; of these: 764s 12 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 1 (14.29%) were unpaired; of these: 764s 1 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s Processing line... 764s Processing line... 764s Processing line... 764s /usr/bin/bowtie2 --cp-min 5 -M 6 --trim5 6 --trim3 4 --cp-ival 3 --local -N 1 -L22 --rfg 36.2416213692808 --rdg 8.6348512288939 --score-min L,7.02637021580779,1.46973476369281 -r -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.als 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s --- Summary --- 764s Read 1 reference strings 764s Checked 0 alignments, 0 edits 764s --------------- 764s PASSED 764s ALSO checking that bowtie2 and bowtie2-align match up 764s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 764s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '1' because it was < 2 characters long 764s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '3' because it was < 2 characters long 764s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '5' because it was < 2 characters long 764s 7 reads; of these: 764s 6 (85.71%) were paired; of these: 764s 6 (100.00%) aligned concordantly 0 times 764s 0 (0.00%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 6 pairs aligned concordantly 0 times; of these: 764s 0 (0.00%) aligned discordantly 1 time 764s ---- 764s 6 pairs aligned 0 times concordantly or discordantly; of these: 764s 12 mates make up the pairs; of these: 764s 12 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 1 (14.29%) were unpaired; of these: 764s 1 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s diff -uw /tmp/Sim.pm.sD3XFvJi.als /tmp/Sim.pm.sD3XFvJi.debug.als 764s /usr/bin/bowtie2 --cp-min 5 -M 6 --trim5 6 --trim3 4 --cp-ival 3 --local -N 1 -L22 --rfg 36.2416213692808 --rdg 8.6348512288939 --score-min L,7.02637021580779,1.46973476369281 -r -p 3 -x /tmp/Sim.pm.sD3XFvJi -1 /tmp/Sim.pm.sD3XFvJi_1.raw -2 /tmp/Sim.pm.sD3XFvJi_2.raw | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als 764s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 764s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 764s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '1' because it was < 2 characters long 764s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '3' because it was < 2 characters long 764s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 764s Warning: skipping mate #1 of read '5' because it was < 2 characters long 764s 7 reads; of these: 764s 6 (85.71%) were paired; of these: 764s 6 (100.00%) aligned concordantly 0 times 764s 0 (0.00%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 6 pairs aligned concordantly 0 times; of these: 764s 0 (0.00%) aligned discordantly 1 time 764s ---- 764s 6 pairs aligned 0 times concordantly or discordantly; of these: 764s 12 mates make up the pairs; of these: 764s 12 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 1 (14.29%) were unpaired; of these: 764s 1 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 0.00% overall alignment rate 764s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.px.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.px.als.sorted 764s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.sD3XFvJi.debug.als | grep -v '^@PG' > /tmp/Sim.pm.sD3XFvJi.debug.als.sorted 764s diff -uw /tmp/Sim.pm.sD3XFvJi.debug.als.sorted /tmp/Sim.pm.sD3XFvJi.px.als.sorted 764s Created DNA generator 764s N frac: 0.026 764s IUPAC frac: 0.009 764s AT/ACGT frac: 0.547 764s A/AT frac: 0.610 764s C/CG frac: 0.700 764s Generating 2 references 764s Generated reference 'Sim.pm.1' of untrimmed length 71, trimmed length 33 764s Generated reference 'Sim.pm.2' of untrimmed length 115, trimmed length 41 764s Wrote references to /tmp/Sim.pm.fu45He6P.fa 764s A: 27 764s C: 17 764s G: 12 764s N: 2 764s R: 1 764s T: 15 764s Executing: /usr/bin/bowtie2-build --dcv 16 --bmaxdivn 6 --offrate 6 --threads 1 /tmp/Sim.pm.fu45He6P.fa /tmp/Sim.pm.fu45He6P 764s *** TEST CASE *** 764s Settings: 764s Output files: "/tmp/Sim.pm.fu45He6P.*.bt2" 764s Line rate: 6 (line is 64 bytes) 764s Lines per side: 1 (side is 64 bytes) 764s Offset rate: 6 (one in 64) 764s FTable chars: 10 764s Strings: unpacked 764s Max bucket size: default 764s Max bucket size, sqrt multiplier: default 764s Max bucket size, len divisor: 6 764s Difference-cover sample period: 16 764s Endianness: little 764s Actual local endianness: little 764s Sanity checking: disabled 764s Assertions: disabled 764s Random seed: 0 764s Sizeofs: void*:8, int:4, long:8, size_t:8 764s Input files DNA, FASTA: 764s /tmp/Sim.pm.fu45He6P.fa 764s Reading reference sizes 764s Building a SMALL index 764s Time reading reference sizes: 00:00:00 764s Calculating joined length 764s Writing header 764s Reserving space for joined string 764s Joining reference sequences 764s Time to join reference sequences: 00:00:00 764s bmax according to bmaxDivN setting: 11 764s Using parameters --bmax 9 --dcv 16 764s Doing ahead-of-time memory usage test 764s Passed! Constructing with these parameters: --bmax 9 --dcv 16 764s Constructing suffix-array element generator 764s Building DifferenceCoverSample 764s Building sPrime 764s Building sPrimeOrder 764s V-Sorting samples 764s V-Sorting samples time: 00:00:00 764s Allocating rank array 764s Ranking v-sort output 764s Ranking v-sort output time: 00:00:00 764s Invoking Larsson-Sadakane on ranks 764s Invoking Larsson-Sadakane on ranks time: 00:00:00 764s Sanity-checking and returning 764s Building samples 764s Reserving space for 18 sample suffixes 764s Generating random suffixes 764s QSorting 18 sample offsets, eliminating duplicates 764s QSorting sample offsets, eliminating duplicates time: 00:00:00 764s Multikey QSorting 16 samples 764s (Using difference cover) 764s Multikey QSorting samples time: 00:00:00 764s Calculating bucket sizes 764s Splitting and merging 764s Splitting and merging time: 00:00:00 764s Avg bucket size: 6.2 (target: 8) 764s Converting suffix-array elements to index image 764s Allocating ftab, absorbFtab 764s Entering Ebwt loop 764s Getting block 1 of 10 764s Reserving size (9) for bucket 1 764s Calculating Z arrays for bucket 1 764s Entering block accumulator loop for bucket 1: 764s bucket 1: 10% 764s bucket 1: 20% 764s bucket 1: 30% 764s bucket 1: 40% 764s bucket 1: 50% 764s bucket 1: 60% 764s bucket 1: 70% 764s bucket 1: 80% 764s bucket 1: 100% 764s Sorting block of length 7 for bucket 1 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 8 for bucket 1 764s Getting block 2 of 10 764s Reserving size (9) for bucket 2 764s Calculating Z arrays for bucket 2 764s Entering block accumulator loop for bucket 2: 764s bucket 2: 10% 764s bucket 2: 20% 764s bucket 2: 30% 764s bucket 2: 40% 764s bucket 2: 50% 764s bucket 2: 60% 764s bucket 2: 70% 764s bucket 2: 80% 764s bucket 2: 100% 764s Sorting block of length 6 for bucket 2 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 7 for bucket 2 764s Getting block 3 of 10 764s Reserving size (9) for bucket 3 764s Calculating Z arrays for bucket 3 764s Entering block accumulator loop for bucket 3: 764s bucket 3: 10% 764s bucket 3: 20% 764s bucket 3: 30% 764s bucket 3: 40% 764s bucket 3: 50% 764s bucket 3: 60% 764s bucket 3: 70% 764s bucket 3: 80% 764s bucket 3: 100% 764s Sorting block of length 6 for bucket 3 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 7 for bucket 3 764s Getting block 4 of 10 764s Reserving size (9) for bucket 4 764s Calculating Z arrays for bucket 4 764s Entering block accumulator loop for bucket 4: 764s bucket 4: 10% 764s bucket 4: 20% 764s bucket 4: 30% 764s bucket 4: 40% 764s bucket 4: 50% 764s bucket 4: 60% 764s bucket 4: 70% 764s bucket 4: 80% 764s bucket 4: 100% 764s Sorting block of length 7 for bucket 4 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 8 for bucket 4 764s Getting block 5 of 10 764s Reserving size (9) for bucket 5 764s Calculating Z arrays for bucket 5 764s Entering block accumulator loop for bucket 5: 764s bucket 5: 10% 764s bucket 5: 20% 764s bucket 5: 30% 764s bucket 5: 40% 764s bucket 5: 50% 764s bucket 5: 60% 764s bucket 5: 70% 764s bucket 5: 80% 764s bucket 5: 100% 764s Sorting block of length 6 for bucket 5 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 7 for bucket 5 764s Getting block 6 of 10 764s Reserving size (9) for bucket 6 764s Calculating Z arrays for bucket 6 764s Entering block accumulator loop for bucket 6: 764s bucket 6: 10% 764s bucket 6: 20% 764s bucket 6: 30% 764s bucket 6: 40% 764s bucket 6: 50% 764s bucket 6: 60% 764s bucket 6: 70% 764s bucket 6: 80% 764s bucket 6: 100% 764s Sorting block of length 6 for bucket 6 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 7 for bucket 6 764s Getting block 7 of 10 764s Reserving size (9) for bucket 7 764s Calculating Z arrays for bucket 7 764s Entering block accumulator loop for bucket 7: 764s bucket 7: 10% 764s bucket 7: 20% 764s bucket 7: 30% 764s bucket 7: 40% 764s bucket 7: 50% 764s bucket 7: 60% 764s bucket 7: 70% 764s bucket 7: 80% 764s bucket 7: 100% 764s Sorting block of length 4 for bucket 7 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 5 for bucket 7 764s Getting block 8 of 10 764s Reserving size (9) for bucket 8 764s Calculating Z arrays for bucket 8 764s Entering block accumulator loop for bucket 8: 764s bucket 8: 10% 764s bucket 8: 20% 764s bucket 8: 30% 764s bucket 8: 40% 764s bucket 8: 50% 764s bucket 8: 60% 764s bucket 8: 70% 764s bucket 8: 80% 764s bucket 8: 100% 764s Sorting block of length 8 for bucket 8 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 9 for bucket 8 764s Getting block 9 of 10 764s Reserving size (9) for bucket 9 764s Calculating Z arrays for bucket 9 764s Entering block accumulator loop for bucket 9: 764s bucket 9: 10% 764s bucket 9: 20% 764s bucket 9: 30% 764s bucket 9: 40% 764s bucket 9: 50% 764s bucket 9: 60% 764s bucket 9: 70% 764s bucket 9: 80% 764s bucket 9: 100% 764s Sorting block of length 8 for bucket 9 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 9 for bucket 9 764s Getting block 10 of 10 764s Reserving size (9) for bucket 10 764s Calculating Z arrays for bucket 10 764s Entering block accumulator loop for bucket 10: 764s bucket 10: 10% 764s bucket 10: 20% 764s bucket 10: 30% 764s bucket 10: 40% 764s bucket 10: 50% 764s bucket 10: 60% 764s bucket 10: 70% 764s bucket 10: 80% 764s bucket 10: 100% 764s Sorting block of length 4 for bucket 10 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 5 for bucket 10 764s Exited Ebwt loop 764s fchr[A]: 0 764s fchr[C]: 27 764s fchr[G]: 44 764s fchr[T]: 56 764s fchr[$]: 71 764s Exiting Ebwt::buildToDisk() 764s Returning from initFromVector 764s Wrote 4194587 bytes to primary EBWT file: /tmp/Sim.pm.fu45He6P.1.bt2.tmp 764s Wrote 12 bytes to secondary EBWT file: /tmp/Sim.pm.fu45He6P.2.bt2.tmp 764s Re-opening _in1 and _in2 as input streams 764s Returning from Ebwt constructor 764s Headers: 764s len: 71 764s bwtLen: 72 764s sz: 18 764s bwtSz: 18 764s lineRate: 6 764s offRate: 6 764s offMask: 0xffffffc0 764s ftabChars: 10 764s eftabLen: 20 764s eftabSz: 80 764s ftabLen: 1048577 764s ftabSz: 4194308 764s offsLen: 2 764s offsSz: 8 764s lineSz: 64 764s sideSz: 64 764s sideBwtSz: 48 764s sideBwtLen: 192 764s numSides: 1 764s numLines: 1 764s ebwtTotLen: 64 764s ebwtTotSz: 64 764s color: 0 764s reverse: 0 764s Total time for call to driver() for forward index: 00:00:00 764s Reading reference sizes 764s Time reading reference sizes: 00:00:00 764s Calculating joined length 764s Writing header 764s Reserving space for joined string 764s Joining reference sequences 764s Time to join reference sequences: 00:00:00 764s Time to reverse reference sequence: 00:00:00 764s bmax according to bmaxDivN setting: 11 764s Using parameters --bmax 9 --dcv 16 764s Doing ahead-of-time memory usage test 764s Passed! Constructing with these parameters: --bmax 9 --dcv 16 764s Constructing suffix-array element generator 764s Building DifferenceCoverSample 764s Building sPrime 764s Building sPrimeOrder 764s V-Sorting samples 764s V-Sorting samples time: 00:00:00 764s Allocating rank array 764s Ranking v-sort output 764s Ranking v-sort output time: 00:00:00 764s Invoking Larsson-Sadakane on ranks 764s Invoking Larsson-Sadakane on ranks time: 00:00:00 764s Sanity-checking and returning 764s Building samples 764s Reserving space for 18 sample suffixes 764s Generating random suffixes 764s QSorting 18 sample offsets, eliminating duplicates 764s QSorting sample offsets, eliminating duplicates time: 00:00:00 764s Multikey QSorting 16 samples 764s (Using difference cover) 764s Multikey QSorting samples time: 00:00:00 764s Calculating bucket sizes 764s Splitting and merging 764s Splitting and merging time: 00:00:00 764s Split 2, merged 8; iterating... 764s Splitting and merging 764s Splitting and merging time: 00:00:00 764s Avg bucket size: 5.54545 (target: 8) 764s Converting suffix-array elements to index image 764s Allocating ftab, absorbFtab 764s Entering Ebwt loop 764s Getting block 1 of 11 764s Reserving size (9) for bucket 1 764s Calculating Z arrays for bucket 1 764s Entering block accumulator loop for bucket 1: 764s bucket 1: 10% 764s bucket 1: 20% 764s bucket 1: 30% 764s bucket 1: 40% 764s bucket 1: 50% 764s bucket 1: 60% 764s bucket 1: 70% 764s bucket 1: 80% 764s bucket 1: 100% 764s Sorting block of length 6 for bucket 1 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 7 for bucket 1 764s Getting block 2 of 11 764s Reserving size (9) for bucket 2 764s Calculating Z arrays for bucket 2 764s Entering block accumulator loop for bucket 2: 764s bucket 2: 10% 764s bucket 2: 20% 764s bucket 2: 30% 764s bucket 2: 40% 764s bucket 2: 50% 764s bucket 2: 60% 764s bucket 2: 70% 764s bucket 2: 80% 764s bucket 2: 100% 764s Sorting block of length 4 for bucket 2 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 5 for bucket 2 764s Getting block 3 of 11 764s Reserving size (9) for bucket 3 764s Calculating Z arrays for bucket 3 764s Entering block accumulator loop for bucket 3: 764s bucket 3: 10% 764s bucket 3: 20% 764s bucket 3: 30% 764s bucket 3: 40% 764s bucket 3: 50% 764s bucket 3: 60% 764s bucket 3: 70% 764s bucket 3: 80% 764s bucket 3: 100% 764s Sorting block of length 6 for bucket 3 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 7 for bucket 3 764s Getting block 4 of 11 764s Reserving size (9) for bucket 4 764s Calculating Z arrays for bucket 4 764s Entering block accumulator loop for bucket 4: 764s bucket 4: 10% 764s bucket 4: 20% 764s bucket 4: 30% 764s bucket 4: 40% 764s bucket 4: 50% 764s bucket 4: 60% 764s bucket 4: 70% 764s bucket 4: 80% 764s bucket 4: 100% 764s Sorting block of length 4 for bucket 4 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 5 for bucket 4 764s Getting block 5 of 11 764s Reserving size (9) for bucket 5 764s Calculating Z arrays for bucket 5 764s Entering block accumulator loop for bucket 5: 764s bucket 5: 10% 764s bucket 5: 20% 764s bucket 5: 30% 764s bucket 5: 40% 764s bucket 5: 50% 764s bucket 5: 60% 764s bucket 5: 70% 764s bucket 5: 80% 764s bucket 5: 100% 764s Sorting block of length 5 for bucket 5 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 6 for bucket 5 764s Getting block 6 of 11 764s Reserving size (9) for bucket 6 764s Calculating Z arrays for bucket 6 764s Entering block accumulator loop for bucket 6: 764s bucket 6: 10% 764s bucket 6: 20% 764s bucket 6: 30% 764s bucket 6: 40% 764s bucket 6: 50% 764s bucket 6: 60% 764s bucket 6: 70% 764s bucket 6: 80% 764s bucket 6: 100% 764s Sorting block of length 8 for bucket 6 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 9 for bucket 6 764s Getting block 7 of 11 764s Reserving size (9) for bucket 7 764s Calculating Z arrays for bucket 7 764s Entering block accumulator loop for bucket 7: 764s bucket 7: 10% 764s bucket 7: 20% 764s bucket 7: 30% 764s bucket 7: 40% 764s bucket 7: 50% 764s bucket 7: 60% 764s bucket 7: 70% 764s bucket 7: 80% 764s bucket 7: 100% 764s Sorting block of length 5 for bucket 7 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 6 for bucket 7 764s Getting block 8 of 11 764s Reserving size (9) for bucket 8 764s Calculating Z arrays for bucket 8 764s Entering block accumulator loop for bucket 8: 764s bucket 8: 10% 764s bucket 8: 20% 764s bucket 8: 30% 764s bucket 8: 40% 764s bucket 8: 50% 764s bucket 8: 60% 764s bucket 8: 70% 764s bucket 8: 80% 764s bucket 8: 100% 764s Sorting block of length 8 for bucket 8 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 9 for bucket 8 764s Getting block 9 of 11 764s Reserving size (9) for bucket 9 764s Calculating Z arrays for bucket 9 764s Entering block accumulator loop for bucket 9: 764s bucket 9: 10% 764s bucket 9: 20% 764s bucket 9: 30% 764s bucket 9: 40% 764s bucket 9: 50% 764s bucket 9: 60% 764s bucket 9: 70% 764s bucket 9: 80% 764s bucket 9: 100% 764s Sorting block of length 3 for bucket 9 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 4 for bucket 9 764s Getting block 10 of 11 764s Reserving size (9) for bucket 10 764s Calculating Z arrays for bucket 10 764s Entering block accumulator loop for bucket 10: 764s bucket 10: 10% 764s bucket 10: 20% 764s bucket 10: 30% 764s bucket 10: 40% 764s bucket 10: 50% 764s bucket 10: 60% 764s bucket 10: 70% 764s bucket 10: 80% 764s bucket 10: 100% 764s Sorting block of length 6 for bucket 10 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 7 for bucket 10 764s Getting block 11 of 11 764s Reserving size (9) for bucket 11 764s Calculating Z arrays for bucket 11 764s Entering block accumulator loop for bucket 11: 764s bucket 11: 10% 764s bucket 11: 20% 764s bucket 11: 30% 764s bucket 11: 40% 764s bucket 11: 50% 764s bucket 11: 60% 764s bucket 11: 70% 764s bucket 11: 80% 764s bucket 11: 100% 764s Sorting block of length 6 for bucket 11 764s (Using difference cover) 764s Sorting block time: 00:00:00 764s Returning block of 7 for bucket 11 764s Exited Ebwt loop 764s fchr[A]: 0 764s fchr[C]: 27 764s fchr[G]: 44 764s fchr[T]: 56 764s fchr[$]: 71 764s Exiting Ebwt::buildToDisk() 764s Returning from initFromVector 764s Wrote 4194587 bytes to primary EBWT file: /tmp/Sim.pm.fu45He6P.rev.1.bt2.tmp 764s Wrote 12 bytes to secondary EBWT file: /tmp/Sim.pm.fu45He6P.rev.2.bt2.tmp 764s Re-opening _in1 and _in2 as input streams 764s Returning from Ebwt constructor 764s Headers: 764s Renaming /tmp/Sim.pm.fu45He6P.3.bt2.tmp to /tmp/Sim.pm.fu45He6P.3.bt2 764s Renaming len: 71 764s bwtLen: 72 764s sz: 18 764s bwtSz: 18 764s lineRate: 6 764s offRate: 6 764s offMask: 0xffffffc0 764s ftabChars: 10 764s eftabLen: 20 764s eftabSz: 80 764s ftabLen: 1048577 764s ftabSz: 4194308 764s offsLen: 2 764s offsSz: 8 764s lineSz: 64 764s sideSz: 64 764s sideBwtSz: 48 764s sideBwtLen: 192 764s numSides: 1 764s numLines: 1 764s ebwtTotLen: 64 764s ebwtTotSz: 64 764s color: 0 764s reverse: 1 764s Total time for backward call to driver() for mirror index: 00:00:00 764s /tmp/Sim.pm.fu45He6P.4.bt2.tmp to /tmp/Sim.pm.fu45He6P.4.bt2 764s Renaming /tmp/Sim.pm.fu45He6P.1.bt2.tmp to /tmp/Sim.pm.fu45He6P.1.bt2 764s Renaming /tmp/Sim.pm.fu45He6P.2.bt2.tmp to /tmp/Sim.pm.fu45He6P.2.bt2 764s Renaming /tmp/Sim.pm.fu45He6P.rev.1.bt2.tmp to /tmp/Sim.pm.fu45He6P.rev.1.bt2 764s Renaming /tmp/Sim.pm.fu45He6P.rev.2.bt2.tmp to /tmp/Sim.pm.fu45He6P.rev.2.bt2 764s Built nucleotide index '/tmp/Sim.pm.fu45He6P' 764s Flattened IUPAC characters 764s Mutating sequence Sim.pm.1 764s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutating sequence Sim.pm.2 764s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutated reference genome to subject genome 764s SNPs introduced: 2 764s Reference gaps introduced: 1 764s Read gaps introduced: 0 764s Rearrangements introduced: 2 764s Created read sampler 764s Sampling 93 reads 764s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 764s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 764s parsing sequence Sim.pm.1... 764s *** Run 1 of 100 764s /usr/bin/bowtie2 --mm --rfg 33.1996879661332,6.0408720739531 --score-min L,3.52165405281847,1.20988763302586 --trim3 1 -D 18 --cp-ival 1 --np 3 -R 2 --cp-min 4 --ma 31.3721583358168 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 764s parsing sequence Sim.pm.2... 764s Parsed 74 reference bases 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Read 50 alignments... 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 764s Read 100 alignments... 764s 93 reads; of these: 764s 91 (97.85%) were paired; of these: 764s 90 (98.90%) aligned concordantly 0 times 764s 1 (1.10%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 90 pairs aligned concordantly 0 times; of these: 764s 1 (1.11%) aligned discordantly 1 time 764s ---- 764s 89 pairs aligned 0 times concordantly or discordantly; of these: 764s 178 mates make up the pairs; of these: 764s 135 (75.84%) aligned 0 times 764s 31 (17.42%) aligned exactly 1 time 764s 12 (6.74%) aligned >1 times 764s 2 (2.15%) were unpaired; of these: 764s 2 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 25.54% overall alignment rate 764s Read 150 alignments... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s ACGCAGTTACCTCCT 764s ACGCAGTTACCTCCT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AACAACGCAGTTACC 764s AACAACGCAGTTACC 764s Processing line... 764s /usr/bin/bowtie2 --mm --rfg 33.1996879661332,6.0408720739531 --score-min L,3.52165405281847,1.20988763302586 --trim3 1 -D 18 --cp-ival 1 --np 3 -R 2 --cp-min 4 --ma 31.3721583358168 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CAGTTACCTCC 764s CAGTTACCTCC 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AACAACGCAGT 764s AACAACGCAGT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s ACCTCCTGAAAAC 764s ACCTCCTGAAAAC 764s Processing line... 764s Processing line... 764s TAATAAC 764s TAATAAC 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s ATAGACGA 764s ATAGACGA 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CAGTTACCTCCT 764s CAGTTACCTCCT 764s Processing line... 764s AACG 764s AACG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CGT 764s CGT 764s Processing line... 764s Processing line... 764s TACCT 764s TACCT 764s Processing line... 764s Processing line... 764s TAACAACGC 764s TAACAACGC 764s Processing line... 764s Processing line... 764s ACCG 764s ACCG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GA 764s GA 764s Processing line... 764s Processing line... 764s AAACATC 764s AAACATC 764s Processing line... 764s Processing line... 764s AG 764s AG 764s Processing line... 764s Processing line... 764s GCAGTTACCTC 764s GCAGTTACCTC 764s Processing line... 764s Processing line... 764s Processing line... 764s CGTCT 764s CGTCT 764s Processing line... 764s Processing line... 764s AGTTACCTCCTGAAA 764s AGTTACCTCCTGAAA 764s Processing line... 764s Processing line... 764s CGCAGTTACCTCCTGA 764s CGCAGTTACCTCCTGA 764s Processing line... 764s Processing line... 764s AAA 764s AAA 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CAACGCAGTTACCTCCT 764s CAACGCAGTTACCTCCT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AGTTACCTCCTGAAAAC 764s AGTTACCTCCTGAAAAC 764s Processing line... 764s Processing line... 764s GAGTGATTAATAAC 764s GAGTGATTAATAAC 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AGTTACCTCCTGAAAA 764s AGTTACCTCCTGAAAA 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CTGAAAACAT 764s CTGAAAACAT 764s Processing line... 764s Processing line... 764s Processing line... 764s GTTACCT 764s GTTACCT 764s Processing line... 764s Processing line... 764s ATGAGTGAT 764s ATGAGTGAT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s TCCTGAA 764s TCCTGAA 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AGA 764s AGA 764s Processing line... 764s CAGTTACCT 764s CAGTTACCT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CCTG 764s CCTG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s TAACAACGCAGTTAC 764s TAACAACGCAGTTAC 764s Processing line... 764s TAA 764s TAA 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AG 764s AG 764s Processing line... 764s Processing line... 764s ATGAGTGATTAATA 764s ATGAGTGATTAATA 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AGT 764s AGT 764s Processing line... 764s Processing line... 764s GTTACCTCCTGAA 764s GTTACCTCCTGAA 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s ACAAC 764s ACAAC 764s Processing line... 764s GACGA 764s GACGA 764s Processing line... 764s ACAT 764s ACAT 764s Processing line... 764s Processing line... 764s ATG 764s ATG 764s Processing line... 764s Processing line... 764s TAACAACGCAGTTACCTCCTGAA 764s TAACAACGCAGTTACCTCCTGAA 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s AACGCAGTTACCTCCTGAAAACA 764s AACGCAGTTACCTCCTGAAAACA 764s Processing line... 764s CAAC 764s CAAC 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s GCAGT 764s GCAGT 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s CTG 764s CTG 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s Processing line... 764s --- Summary --- 764s Read 1 reference strings 764s Checked 47 alignments, 0 edits 764s --------------- 764s PASSED 764s ALSO checking that bowtie2 and bowtie2-align match up 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 764s 93 reads; of these: 764s 91 (97.85%) were paired; of these: 764s 90 (98.90%) aligned concordantly 0 times 764s 1 (1.10%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 90 pairs aligned concordantly 0 times; of these: 764s 1 (1.11%) aligned discordantly 1 time 764s ---- 764s 89 pairs aligned 0 times concordantly or discordantly; of these: 764s 178 mates make up the pairs; of these: 764s 135 (75.84%) aligned 0 times 764s 31 (17.42%) aligned exactly 1 time 764s 12 (6.74%) aligned >1 times 764s 2 (2.15%) were unpaired; of these: 764s 2 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 25.54% overall alignment rate 764s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 764s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 764s /usr/bin/bowtie2 --mm --rfg 33.1996879661332,6.0408720739531 --score-min L,3.52165405281847,1.20988763302586 --trim3 1 -D 18 --cp-ival 1 --np 3 -R 2 --cp-min 4 --ma 31.3721583358168 --qseq -p 2 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 764s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 764s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 764s 93 reads; of these: 764s 91 (97.85%) were paired; of these: 764s 90 (98.90%) aligned concordantly 0 times 764s 1 (1.10%) aligned concordantly exactly 1 time 764s 0 (0.00%) aligned concordantly >1 times 764s ---- 764s 90 pairs aligned concordantly 0 times; of these: 764s 1 (1.11%) aligned discordantly 1 time 764s ---- 764s 89 pairs aligned 0 times concordantly or discordantly; of these: 764s 178 mates make up the pairs; of these: 764s 135 (75.84%) aligned 0 times 764s 31 (17.42%) aligned exactly 1 time 764s 12 (6.74%) aligned >1 times 764s 2 (2.15%) were unpaired; of these: 764s 2 (100.00%) aligned 0 times 764s 0 (0.00%) aligned exactly 1 time 764s 0 (0.00%) aligned >1 times 764s 25.54% overall alignment rate 764s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 764s Flattened IUPAC characters 764s Mutating sequence Sim.pm.2 764s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutating sequence Sim.pm.1 764s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 764s Finished SNPs 764s Finished ref gaps 764s Finished read gaps 764s Mutated reference genome to subject genome 764s SNPs introduced: 8 764s Reference gaps introduced: 2 764s Read gaps introduced: 0 764s Rearrangements introduced: 0 764s Created read sampler 764s Sampling 86 reads 764s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 764s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 764s parsing sequence Sim.pm.1... 764s parsing sequence Sim.pm.2... 764s Parsed 74 reference bases 764s *** Run 2 of 100 764s /usr/bin/bowtie2 --cp-ival 3 --cp-min 3 --nofw --rfg 38.9401176124392 --score-min L,5.2296517167801,5.85178842088302 --mm --trim5 3 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 764s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '5' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 764s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '8' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 764s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '12' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 764s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '22' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 764s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '29' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 764s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '34' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 764s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '51' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 764s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 764s Warning: skipping mate #1 of read '53' because it was < 2 characters long 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 764s Read 50 alignments... 764s Read 100 alignments... 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 764s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 765s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '73' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 765s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '74' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 765s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '82' because it was < 2 characters long 765s Warning: skipping mate #2 of read '82' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 765s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '84' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 765s 86 reads; of these: 765s 76 (88.37%) were paired; of these: 765s 75 (98.68%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 1 (1.32%) aligned concordantly >1 times 765s ---- 765s 75 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 75 pairs aligned 0 times concordantly or discordantly; of these: 765s 150 mates make up the pairs; of these: 765s 131 (87.33%) aligned 0 times 765s 14 (9.33%) aligned exactly 1 time 765s 5 (3.33%) aligned >1 times 765s 10 (11.63%) were unpaired; of these: 765s 10 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 12.96% overall alignment rate 765s Read 150 alignments... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s ATATGAGTGATTAATAACGTCTG 765s ATATGAGTGATTAATAACGTCTG 765s Processing line... 765s Processing line... 765s CTG 765s CTG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GAGA 765s GAGA 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GAG 765s GAG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s AACAACG 765s AACAACG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TTACCTCCT 765s TTACCTCCT 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s CAT 765s CAT 765s Processing line... 765s Processing line... 765s AACGC 765s AACGC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s /usr/bin/bowtie2 --cp-ival 3 --cp-min 3 --nofw --rfg 38.9401176124392 --score-min L,5.2296517167801,5.85178842088302 --mm --trim5 3 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s ACAACGCAGTTACCTCCT 765s ACAACGCAGTTACCTCCT 765s Processing line... 765s Processing line... 765s TCC 765s TCC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s AACA 765s AACA 765s Processing line... 765s Processing line... 765s TT 765s TT 765s Processing line... 765s GTT 765s GTT 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s ACAAC 765s ACAAC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TAACAACGCAGTTACCTCCTG 765s TAACAACGCAGTTACCTCCTG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TAACAACG 765s TAACAACG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s CAGTTA 765s CAGTTA 765s Processing line... 765s Processing line... 765s AACAACGC 765s AACAACGC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TAACAACGCAGT 765s TAACAACGCAGT 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s AG 765s AG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GCAGTTACC 765s GCAGTTACC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s --- Summary --- 765s Read 1 reference strings 765s Checked 21 alignments, 0 edits 765s --------------- 765s PASSED 765s ALSO checking that bowtie2 and bowtie2-align match up 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '5' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '8' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '12' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '22' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '29' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '34' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 765s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '51' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 765s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '53' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 765s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '73' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 765s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '74' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 765s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '82' because it was < 2 characters long 765s Warning: skipping mate #2 of read '82' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 765s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '84' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 765s 86 reads; of these: 765s 76 (88.37%) were paired; of these: 765s 75 (98.68%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 1 (1.32%) aligned concordantly >1 times 765s ---- 765s 75 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 75 pairs aligned 0 times concordantly or discordantly; of these: 765s 150 mates make up the pairs; of these: 765s 131 (87.33%) aligned 0 times 765s 14 (9.33%) aligned exactly 1 time 765s 5 (3.33%) aligned >1 times 765s 10 (11.63%) were unpaired; of these: 765s 10 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 12.96% overall alignment rate 765s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 765s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 765s /usr/bin/bowtie2 --cp-ival 3 --cp-min 3 --nofw --rfg 38.9401176124392 --score-min L,5.2296517167801,5.85178842088302 --mm --trim5 3 -f -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '5' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '8' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '12' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '22' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '29' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '34' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 765s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '51' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 765s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '53' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 765s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '73' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 765s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '74' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 765s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '82' because it was < 2 characters long 765s Warning: skipping mate #2 of read '82' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 765s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '84' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 765s 86 reads; of these: 765s 76 (88.37%) were paired; of these: 765s 75 (98.68%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 1 (1.32%) aligned concordantly >1 times 765s ---- 765s 75 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 75 pairs aligned 0 times concordantly or discordantly; of these: 765s 150 mates make up the pairs; of these: 765s 131 (87.33%) aligned 0 times 765s 14 (9.33%) aligned exactly 1 time 765s 5 (3.33%) aligned >1 times 765s 10 (11.63%) were unpaired; of these: 765s 10 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 12.96% overall alignment rate 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 765s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 765s /usr/bin/bowtie2 --cp-ival 3 --cp-min 3 --nofw --rfg 38.9401176124392 --score-min L,5.2296517167801,5.85178842088302 --mm --trim5 3 -f -p 4 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 765s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '5' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: skipping mate #1 of read '8' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '8' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '12' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '22' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '29' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '34' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 765s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '51' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 765s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '53' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 765s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '73' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 765s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '74' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 765s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '82' because it was < 2 characters long 765s Warning: skipping mate #2 of read '82' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 765s Warning: skipping mate #1 of read '84' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '84' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 765s 86 reads; of these: 765s 76 (88.37%) were paired; of these: 765s 75 (98.68%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 1 (1.32%) aligned concordantly >1 times 765s ---- 765s 75 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 75 pairs aligned 0 times concordantly or discordantly; of these: 765s 150 mates make up the pairs; of these: 765s 131 (87.33%) aligned 0 times 765s 14 (9.33%) aligned exactly 1 time 765s 5 (3.33%) aligned >1 times 765s 10 (11.63%) were unpaired; of these: 765s 10 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 12.96% overall alignment rate 765s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 765s Flattened IUPAC characters 765s Mutating sequence Sim.pm.2 765s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutating sequence Sim.pm.1 765s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutated reference genome to subject genome 765s SNPs introduced: 3 765s Reference gaps introduced: 0 765s Read gaps introduced: 1 765s Rearrangements introduced: 1 765s Created read sampler 765s Sampling 46 reads 765s *** Run 3 of 100 765s /usr/bin/bowtie2 -i C,3.72003995869467 --np 1 --ma 5.92875987521587 --cp-min 3 --mm --score-min L,1.97143822469388,4.46992090341788 --rfg 33.8816354153394,12.8561234030735 --gbar 4 --trim3 0 --nofw --cp-ival 1 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 765s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 765s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 765s parsing sequence Sim.pm.1... 765s parsing sequence Sim.pm.2... 765s Parsed 74 reference bases 765s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '21' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 765s 46 reads; of these: 765s 46 (100.00%) were paired; of these: 765s 46 (100.00%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 0 (0.00%) aligned concordantly >1 times 765s ---- 765s 46 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 46 pairs aligned 0 times concordantly or discordantly; of these: 765s 92 mates make up the pairs; of these: 765s 84 (91.30%) aligned 0 times 765s 7 (7.61%) aligned exactly 1 time 765s 1 (1.09%) aligned >1 times 765s 8.70% overall alignment rate 765s Read 50 alignments... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TTACCTCCTGAAAACATC 765s TTACCTCCTGAAAACATC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TTACCTCCTGAAAA 765s TTACCTCCTGAAAA 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s CTGAAAACATCC 765s CTGAAAACATCC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s /usr/bin/bowtie2 -i C,3.72003995869467 --np 1 --ma 5.92875987521587 --cp-min 3 --mm --score-min L,1.97143822469388,4.46992090341788 --rfg 33.8816354153394,12.8561234030735 --gbar 4 --trim3 0 --nofw --cp-ival 1 -r -p 4 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 765s Processing line... 765s Processing line... 765s AAACATCC 765s AAACATCC 765s Processing line... 765s Processing line... 765s CGCAGTTAC 765s CGCAGTTAC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TACCTC 765s TACCTC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GATTAAT 765s GATTAAT 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s CT 765s CT 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s --- Summary --- 765s Read 1 reference strings 765s Checked 8 alignments, 0 edits 765s --------------- 765s PASSED 765s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 765s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '21' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 765s 46 reads; of these: 765s 46 (100.00%) were paired; of these: 765s 46 (100.00%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 0 (0.00%) aligned concordantly >1 times 765s ---- 765s 46 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 46 pairs aligned 0 times concordantly or discordantly; of these: 765s 92 mates make up the pairs; of these: 765s 84 (91.30%) aligned 0 times 765s 7 (7.61%) aligned exactly 1 time 765s 1 (1.09%) aligned >1 times 765s 8.70% overall alignment rate 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 765s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 765s /usr/bin/bowtie2 -i C,3.72003995869467 --np 1 --ma 5.92875987521587 --cp-min 3 --mm --score-min L,1.97143822469388,4.46992090341788 --rfg 33.8816354153394,12.8561234030735 --gbar 4 --trim3 0 --nofw --cp-ival 1 -r -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 765s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 765s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '21' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 765s 46 reads; of these: 765s 46 (100.00%) were paired; of these: 765s 46 (100.00%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 0 (0.00%) aligned concordantly >1 times 765s ---- 765s 46 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 46 pairs aligned 0 times concordantly or discordantly; of these: 765s 92 mates make up the pairs; of these: 765s 84 (91.30%) aligned 0 times 765s 7 (7.61%) aligned exactly 1 time 765s 1 (1.09%) aligned >1 times 765s 8.70% overall alignment rate 765s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 765s Flattened IUPAC characters 765s Mutating sequence Sim.pm.2 765s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutating sequence Sim.pm.1 765s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutated reference genome to subject genome 765s SNPs introduced: 0 765s Reference gaps introduced: 0 765s Read gaps introduced: 0 765s Rearrangements introduced: 0 765s Created read sampler 765s Sampling 182 reads 765s *** Run 4 of 100 765s /usr/bin/bowtie2 --norc --np 9 -R 2 --cp-min 3 -a --score-min L,5.57462141515818,9.41051688273155 --gbar 3 --trim3 1 --nofw -D 25 --cp-ival 3 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 765s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 765s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 765s parsing sequence Sim.pm.1... 765s parsing sequence Sim.pm.2... 765s Parsed 74 reference bases 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '8' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '44' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 765s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '50' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 765s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '78' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 765s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '89' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 765s Warning: skipping mate #1 of read '101' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '101' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 765s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '102' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 765s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '110' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 765s Warning: skipping mate #2 of read '123' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '123' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 765s Warning: skipping mate #1 of read '125' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '125' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '125' because it was < 2 characters long 765s Warning: skipping mate #2 of read '125' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 765s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '150' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 765s Warning: skipping mate #2 of read '152' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '152' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 765s Warning: skipping mate #2 of read '153' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '153' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 765s Read 50 alignments... 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 765s Read 100 alignments... 765s /usr/bin/bowtie2 --norc --np 9 -R 2 --cp-min 3 -a --score-min L,5.57462141515818,9.41051688273155 --gbar 3 --trim3 1 --nofw -D 25 --cp-ival 3 -r -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 765s Warning: skipping mate #1 of read '164' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '164' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 765s 182 reads; of these: 765s 178 (97.80%) were paired; of these: 765s 178 (100.00%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 0 (0.00%) aligned concordantly >1 times 765s ---- 765s 178 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 178 pairs aligned 0 times concordantly or discordantly; of these: 765s 356 mates make up the pairs; of these: 765s 356 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 4 (2.20%) were unpaired; of these: 765s 4 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 0.00% overall alignment rate 765s Read 150 alignments... 765s Read 200 alignments... 765s Read 250 alignments... 765s Read 300 alignments... 765s Read 350 alignments... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing 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Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s --- Summary --- 765s Read 1 reference strings 765s Checked 0 alignments, 0 edits 765s --------------- 765s PASSED 765s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '8' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '44' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 765s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '50' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 765s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '78' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 765s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 765s /usr/bin/bowtie2 --norc --np 9 -R 2 --cp-min 3 -a --score-min L,5.57462141515818,9.41051688273155 --gbar 3 --trim3 1 --nofw -D 25 --cp-ival 3 -r -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 765s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '89' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 765s Warning: skipping mate #1 of read '101' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '101' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 765s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '102' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 765s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '110' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 765s Warning: skipping mate #2 of read '123' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '123' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 765s Warning: skipping mate #1 of read '125' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '125' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '125' because it was < 2 characters long 765s Warning: skipping mate #2 of read '125' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 765s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '150' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 765s Warning: skipping mate #2 of read '152' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '152' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 765s Warning: skipping mate #2 of read '153' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '153' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 765s Warning: skipping mate #1 of read '164' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '164' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 765s 182 reads; of these: 765s 178 (97.80%) were paired; of these: 765s 178 (100.00%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 0 (0.00%) aligned concordantly >1 times 765s ---- 765s 178 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 178 pairs aligned 0 times concordantly or discordantly; of these: 765s 356 mates make up the pairs; of these: 765s 356 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 4 (2.20%) were unpaired; of these: 765s 4 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 0.00% overall alignment rate 765s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 765s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '8' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 765s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '44' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 765s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '50' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 765s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '78' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 765s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '89' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 765s Warning: skipping mate #1 of read '101' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '101' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 765s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '102' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 765s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '110' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 765s Warning: skipping mate #2 of read '123' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '123' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 765s Warning: skipping mate #1 of read '125' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '125' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '125' because it was < 2 characters long 765s Warning: skipping mate #2 of read '125' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 765s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '150' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 765s Warning: skipping mate #2 of read '152' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '152' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 765s Warning: skipping mate #2 of read '153' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #2 of read '153' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 765s Warning: skipping mate #1 of read '164' because length (1) <= # seed mismatches (0) 765s Warning: skipping mate #1 of read '164' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 765s 182 reads; of these: 765s 178 (97.80%) were paired; of these: 765s 178 (100.00%) aligned concordantly 0 times 765s 0 (0.00%) aligned concordantly exactly 1 time 765s 0 (0.00%) aligned concordantly >1 times 765s ---- 765s 178 pairs aligned concordantly 0 times; of these: 765s 0 (0.00%) aligned discordantly 1 time 765s ---- 765s 178 pairs aligned 0 times concordantly or discordantly; of these: 765s 356 mates make up the pairs; of these: 765s 356 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 4 (2.20%) were unpaired; of these: 765s 4 (100.00%) aligned 0 times 765s 0 (0.00%) aligned exactly 1 time 765s 0 (0.00%) aligned >1 times 765s 0.00% overall alignment rate 765s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 765s Flattened IUPAC characters 765s Mutating sequence Sim.pm.2 765s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s *** Run 5 of 100 765s /usr/bin/bowtie2 --score-min L,1.43885304839467,8.49982581217084 --mm -a --trim5 3 -N 1 -L29 --cp-min 3 --cp-ival 1 -D 44 --trim3 4 --qseq -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq 765s Finished ref gaps 765s Finished read gaps 765s Mutating sequence Sim.pm.1 765s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutated reference genome to subject genome 765s SNPs introduced: 0 765s Reference gaps introduced: 1 765s Read gaps introduced: 0 765s Rearrangements introduced: 0 765s Created read sampler 765s Sampling 35 reads 765s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 765s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 765s parsing sequence Sim.pm.1... 765s parsing sequence Sim.pm.2... 765s Parsed 74 reference bases 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 765s 35 reads; of these: 765s 35 (100.00%) were unpaired; of these: 765s 29 (82.86%) aligned 0 times 765s 3 (8.57%) aligned exactly 1 time 765s 3 (8.57%) aligned >1 times 765s 17.14% overall alignment rate 765s Read 50 alignments... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s TCTG 765s TCTG 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s GA 765s GA 765s Processing line... 765s GA 765s GA 765s Processing line... 765s GA 765s GA 765s Processing line... 765s TC 765s TC 765s Processing line... 765s TC 765s TC 765s Processing line... 765s TC 765s TC 765s Processing line... 765s GA 765s GA 765s Processing line... 765s GA 765s GA 765s Processing line... 765s GA 765s GA 765s Processing line... 765s GA 765s GA 765s Processing line... 765s CC 765s CC 765s Processing line... 765s CC 765s CC 765s Processing line... 765s CC 765s CC 765s Processing line... 765s CC 765s CC 765s Processing line... 765s Processing line... 765s Processing line... 765s GTG 765s GTG 765s Processing line... 765s AGTTAC 765s AGTTAC 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s Processing line... 765s CC 765s CC 765s Processing line... 765s CC 765s CC 765s Processing line... 765s CC 765s CC 765s Processing line... 765s CC 765s CC 765s Processing line... 765s Processing line... 765s --- Summary --- 765s Read 1 reference strings 765s Checked 21 alignments, 0 edits 765s --------------- 765s PASSED 765s ALSO checking that bowtie2 and bowtie2-align match up 765s /usr/bin/bowtie2 --score-min L,1.43885304839467,8.49982581217084 --mm -a --trim5 3 -N 1 -L29 --cp-min 3 --cp-ival 1 -D 44 --trim3 4 --qseq -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 765s 35 reads; of these: 765s 35 (100.00%) were unpaired; of these: 765s 29 (82.86%) aligned 0 times 765s 3 (8.57%) aligned exactly 1 time 765s 3 (8.57%) aligned >1 times 765s 17.14% overall alignment rate 765s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 765s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 765s /usr/bin/bowtie2 --score-min L,1.43885304839467,8.49982581217084 --mm -a --trim5 3 -N 1 -L29 --cp-min 3 --cp-ival 1 -D 44 --trim3 4 --qseq -p 3 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 765s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (1) 765s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 765s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 765s 35 reads; of these: 765s 35 (100.00%) were unpaired; of these: 765s 29 (82.86%) aligned 0 times 765s 3 (8.57%) aligned exactly 1 time 765s 3 (8.57%) aligned >1 times 765s 17.14% overall alignment rate 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 765s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 765s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 765s Flattened IUPAC characters 765s Mutating sequence Sim.pm.2 765s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutating sequence Sim.pm.1 765s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 765s Finished SNPs 765s Finished ref gaps 765s Finished read gaps 765s Mutated reference genome to subject genome 765s SNPs introduced: 6 765s Reference gaps introduced: 1 765s Read gaps introduced: 0 765s Rearrangements introduced: 0 765s Created read sampler 765s Sampling 124 reads 765s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 765s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 765s parsing sequence Sim.pm.1... 765s parsing sequence Sim.pm.2... 765s Parsed 74 reference bases 765s *** Run 6 of 100 765s /usr/bin/bowtie2 --norc --np 4 -M 2 --cp-min 6 --score-min L,4.30166698975567,3.70494607366641 --rfg 39.5350105047579 --mm --n-ceil 0.0847237274057776,0.482144901055059 --cp-ival 1 --local -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 766s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 766s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '53' because it was < 2 characters long 766s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '73' because it was < 2 characters long 766s Read 50 alignments... 766s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '88' because it was < 2 characters long 766s Read 100 alignments... 766s 124 reads; of these: 766s 124 (100.00%) were paired; of these: 766s 124 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 124 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 124 pairs aligned 0 times concordantly or discordantly; of these: 766s 248 mates make up the pairs; of these: 766s 248 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s Read 150 alignments... 766s Read 200 alignments... 766s Read 250 alignments... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s 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Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 0 alignments, 0 edits 766s --------------- 766s PASSED 766s ALSO checking that bowtie2 and bowtie2-align match up 766s /usr/bin/bowtie2 --norc --np 4 -M 2 --cp-min 6 --score-min L,4.30166698975567,3.70494607366641 --rfg 39.5350105047579 --mm --n-ceil 0.0847237274057776,0.482144901055059 --cp-ival 1 --local -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 766s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 766s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '53' because it was < 2 characters long 766s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '73' because it was < 2 characters long 766s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '88' because it was < 2 characters long 766s 124 reads; of these: 766s 124 (100.00%) were paired; of these: 766s 124 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 124 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 124 pairs aligned 0 times concordantly or discordantly; of these: 766s 248 mates make up the pairs; of these: 766s 248 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 766s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 766s /usr/bin/bowtie2 --norc --np 4 -M 2 --cp-min 6 --score-min L,4.30166698975567,3.70494607366641 --rfg 39.5350105047579 --mm --n-ceil 0.0847237274057776,0.482144901055059 --cp-ival 1 --local -f -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 766s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 766s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '53' because it was < 2 characters long 766s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '73' because it was < 2 characters long 766s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '88' because it was < 2 characters long 766s 124 reads; of these: 766s 124 (100.00%) were paired; of these: 766s 124 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 124 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 124 pairs aligned 0 times concordantly or discordantly; of these: 766s 248 mates make up the pairs; of these: 766s 248 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 766s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.2 766s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.1 766s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 4 766s Reference gaps introduced: 0 766s Read gaps introduced: 0 766s Rearrangements introduced: 0 766s Created read sampler 766s Sampling 65 reads 766s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 766s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 74 reference bases 766s *** Run 7 of 100 766s /usr/bin/bowtie2 --mm --rdg 25.552291135278 --score-min L,7.99109431786603,9.30807151048727 -R 3 --trim3 9 -N 0 -L12 --ma 20.6616944657844 --cp-ival 1 --n-ceil 1.22407296208954,0.073475804527031 --cp-min 4 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 766s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '11' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 766s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '14' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 766s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '19' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 766s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '32' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 766s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '33' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 766s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '36' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 766s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '39' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 766s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '41' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 766s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '45' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 766s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '48' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 766s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '56' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 766s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '57' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 766s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '59' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 766s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '60' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 766s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '61' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 766s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '62' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 766s 65 reads; of these: 766s 50 (76.92%) were paired; of these: 766s 50 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 50 pairs aligned concordantly 0 times; of these: 766s 1 (2.00%) aligned discordantly 1 time 766s ---- 766s 49 pairs aligned 0 times concordantly or discordantly; of these: 766s 98 mates make up the pairs; of these: 766s 84 (85.71%) aligned 0 times 766s 11 (11.22%) aligned exactly 1 time 766s 3 (3.06%) aligned >1 times 766s 15 (23.08%) were unpaired; of these: 766s 14 (93.33%) aligned 0 times 766s 1 (6.67%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 14.78% overall alignment rate 766s Read 50 alignments... 766s Read 100 alignments... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s ACGCAGTTAC 766s ACGCAGTTAC 766s Processing line... 766s ACCTCC 766s ACCTCC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TAACAAC 766s TAACAAC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s ACAT 766s ACAT 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CCTGAAAACAT 766s CCTGAAAACAT 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CCTCCTGAAAA 766s CCTCCTGAAAA 766s Processing line... 766s Processing line... 766s /usr/bin/bowtie2 --mm --rdg 25.552291135278 --score-min L,7.99109431786603,9.30807151048727 -R 3 --trim3 9 -N 0 -L12 --ma 20.6616944657844 --cp-ival 1 --n-ceil 1.22407296208954,0.073475804527031 --cp-min 4 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TCCTGAA 766s TCCTGAA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GA 766s GA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TTACCTCCT 766s TTACCTCCT 766s Processing line... 766s Processing line... 766s ATGA 766s ATGA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s AC 766s AC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CTCCTGAA 766s CTCCTGAA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CTGA 766s CTGA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TCCTGAAAACATCC 766s TCCTGAAAACATCC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GAC 766s GAC 766s Processing line... 766s Processing line... 766s ACATCC 766s ACATCC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CCTCCTGAAAACATC 766s CCTCCTGAAAACATC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 17 alignments, 0 edits 766s --------------- 766s PASSED 766s ALSO checking that bowtie2 and bowtie2-align match up 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 766s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '11' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 766s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '14' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 766s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '19' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 766s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '32' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 766s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '33' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 766s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '36' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 766s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '39' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 766s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '41' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 766s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '45' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 766s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '48' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 766s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '56' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 766s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '57' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 766s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '59' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 766s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '60' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 766s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '61' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 766s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '62' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 766s 65 reads; of these: 766s 50 (76.92%) were paired; of these: 766s 50 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 50 pairs aligned concordantly 0 times; of these: 766s 1 (2.00%) aligned discordantly 1 time 766s ---- 766s 49 pairs aligned 0 times concordantly or discordantly; of these: 766s 98 mates make up the pairs; of these: 766s 84 (85.71%) aligned 0 times 766s 11 (11.22%) aligned exactly 1 time 766s 3 (3.06%) aligned >1 times 766s 15 (23.08%) were unpaired; of these: 766s 14 (93.33%) aligned 0 times 766s 1 (6.67%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 14.78% overall alignment rate 766s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 766s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 766s /usr/bin/bowtie2 --mm --rdg 25.552291135278 --score-min L,7.99109431786603,9.30807151048727 -R 3 --trim3 9 -N 0 -L12 --ma 20.6616944657844 --cp-ival 1 --n-ceil 1.22407296208954,0.073475804527031 --cp-min 4 -q -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 766s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '11' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 766s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '14' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 766s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '19' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 766s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '32' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 766s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '33' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 766s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '36' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 766s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '39' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 766s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '41' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 766s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '45' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 766s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '48' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 766s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '56' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 766s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '57' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 766s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '59' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 766s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '60' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 766s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '61' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 766s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '62' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 766s 65 reads; of these: 766s 50 (76.92%) were paired; of these: 766s 50 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 50 pairs aligned concordantly 0 times; of these: 766s 1 (2.00%) aligned discordantly 1 time 766s ---- 766s 49 pairs aligned 0 times concordantly or discordantly; of these: 766s 98 mates make up the pairs; of these: 766s 84 (85.71%) aligned 0 times 766s 11 (11.22%) aligned exactly 1 time 766s 3 (3.06%) aligned >1 times 766s 15 (23.08%) were unpaired; of these: 766s 14 (93.33%) aligned 0 times 766s 1 (6.67%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 14.78% overall alignment rate 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 766s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.1 766s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.2 766s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 8 766s Reference gaps introduced: 0 766s Read gaps introduced: 0 766s Rearrangements introduced: 2 766s Created read sampler 766s Sampling 68 reads 766s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 766s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 74 reference bases 766s *** Run 8 of 100 766s /usr/bin/bowtie2 --cp-ival 1 --cp-min 3 --ma 20.3624473273792 -R 3 --gbar 6 --np 2 --rdg 6.65103272317806 --rfg 8.48022327237715,9.04405371972572 --score-min L,2.25827776265964,2.41800127901608 -M 2 --mm --trim5 6 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 766s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 766s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '23' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 766s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '42' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 766s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '46' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 766s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '49' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 766s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '50' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 766s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '60' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 766s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '61' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 766s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '62' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 766s Read 50 alignments... 766s Read 100 alignments... 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 766s 68 reads; of these: 766s 64 (94.12%) were paired; of these: 766s 64 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 64 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 64 pairs aligned 0 times concordantly or discordantly; of these: 766s 128 mates make up the pairs; of these: 766s 116 (90.62%) aligned 0 times 766s 8 (6.25%) aligned exactly 1 time 766s 4 (3.12%) aligned >1 times 766s 4 (5.88%) were unpaired; of these: 766s 2 (50.00%) aligned 0 times 766s 1 (25.00%) aligned exactly 1 time 766s 1 (25.00%) aligned >1 times 766s 10.61% overall alignment rate 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GCAGT 766s GCAGT 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TACCTCCTG 766s TACCTCCTG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s ATA 766s ATA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CGCAGTTACCTC 766s CGCAGTTACCTC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s AC 766s AC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CA 766s CA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GTTAC 766s GTTAC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CC 766s CC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CGCAGTTACCTC 766s CGCAGTTACCTC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s AAAA 766s AAAA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CGCAG 766s CGCAG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TAATAA 766s TAATAA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TA 766s TA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s ACGCAGT 766s ACGCAGT 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 14 alignments, 0 edits 766s --------------- 766s PASSED 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.1 766s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.2 766s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 5 766s Reference gaps introduced: 0 766s Read gaps introduced: 0 766s Rearrangements introduced: 0 766s Created read sampler 766s Sampling 61 reads 766s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 766s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 74 reference bases 766s *** Run 9 of 100 766s /usr/bin/bowtie2 --mm --score-min L,3.08817884628438,5.97601670490644 --norc --trim3 1 --cp-min 2 --cp-ival 2 --ma 21.2930267215275 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 766s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '2' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 766s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '3' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 766s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '5' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 766s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '10' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 766s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '16' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 766s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '23' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 766s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '30' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 766s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '45' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 766s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '53' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 766s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '59' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 766s 61 reads; of these: 766s 60 (98.36%) were paired; of these: 766s 60 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 60 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 60 pairs aligned 0 times concordantly or discordantly; of these: 766s 120 mates make up the pairs; of these: 766s 113 (94.17%) aligned 0 times 766s 5 (4.17%) aligned exactly 1 time 766s 2 (1.67%) aligned >1 times 766s 1 (1.64%) were unpaired; of these: 766s 1 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 5.79% overall alignment rate 766s Read 50 alignments... 766s Read 100 alignments... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s AACAT 766s AACAT 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s AACGCAGTTACCT 766s AACGCAGTTACCT 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TT 766s TT 766s Processing line... 766s Processing line... 766s AACGCAGTTACCTCCTG 766s AACGCAGTTACCTCCTG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s GTTACCTCCTG 766s GTTACCTCCTG 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s CAA 766s CAA 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TT 766s TT 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 7 alignments, 0 edits 766s --------------- 766s PASSED 766s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 766s /usr/bin/bowtie2 --mm --score-min L,3.08817884628438,5.97601670490644 --norc --trim3 1 --cp-min 2 --cp-ival 2 --ma 21.2930267215275 -q -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 766s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '2' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 766s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '3' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 766s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '5' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 766s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '10' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 766s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '16' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 766s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '23' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 766s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '30' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 766s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '45' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 766s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '53' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 766s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '59' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 766s 61 reads; of these: 766s 60 (98.36%) were paired; of these: 766s 60 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 60 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 60 pairs aligned 0 times concordantly or discordantly; of these: 766s 120 mates make up the pairs; of these: 766s 113 (94.17%) aligned 0 times 766s 5 (4.17%) aligned exactly 1 time 766s 2 (1.67%) aligned >1 times 766s 1 (1.64%) were unpaired; of these: 766s 1 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 5.79% overall alignment rate 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 766s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 766s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 766s /usr/bin/bowtie2 --mm --score-min L,3.08817884628438,5.97601670490644 --norc --trim3 1 --cp-min 2 --cp-ival 2 --ma 21.2930267215275 -q -p 2 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 766s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '2' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 766s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '3' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 766s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '5' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 766s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '10' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 766s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '16' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 766s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '23' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 766s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '30' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 766s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '45' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 766s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '53' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 766s Warning: skipping mate #1 of read '59' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '59' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 766s 61 reads; of these: 766s 60 (98.36%) were paired; of these: 766s 60 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 60 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 60 pairs aligned 0 times concordantly or discordantly; of these: 766s 120 mates make up the pairs; of these: 766s 113 (94.17%) aligned 0 times 766s 5 (4.17%) aligned exactly 1 time 766s 2 (1.67%) aligned >1 times 766s 1 (1.64%) were unpaired; of these: 766s 1 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 5.79% overall alignment rate 766s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.1 766s Introducing 1 SNPs, 1/1 ref/read gaps, and 1 rearrangements 766s *** Run 10 of 100 766s /usr/bin/bowtie2 --trim3 7 --mp 6.18852478080644,2.58926622806472 --cp-ival 1 --local --n-ceil 1.4532467033835,0.568230876372952 --score-min L,9.30037485693203,2.58531781507284 --gbar 2 --cp-min 2 -i L,0.179260422818892 --trim5 5 --np 6 --qseq -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.2 766s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 4 766s Reference gaps introduced: 1 766s Read gaps introduced: 1 766s Rearrangements introduced: 1 766s Created read sampler 766s Sampling 20 reads 766s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 766s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 74 reference bases 766s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 766s 20 reads; of these: 766s 20 (100.00%) were unpaired; of these: 766s 20 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 0 alignments, 0 edits 766s --------------- 766s PASSED 766s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 766s /usr/bin/bowtie2 --trim3 7 --mp 6.18852478080644,2.58926622806472 --cp-ival 1 --local --n-ceil 1.4532467033835,0.568230876372952 --score-min L,9.30037485693203,2.58531781507284 --gbar 2 --cp-min 2 -i L,0.179260422818892 --trim5 5 --np 6 --qseq -p 4 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 766s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 766s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 766s 20 reads; of these: 766s 20 (100.00%) were unpaired; of these: 766s 20 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 766s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 766s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.1 766s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.2 766s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 3 766s Reference gaps introduced: 0 766s Read gaps introduced: 0 766s Rearrangements introduced: 0 766s Created read sampler 766s Sampling 36 reads 766s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 766s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 74 reference bases 766s *** Run 11 of 100 766s /usr/bin/bowtie2 --cp-min 10 -R 3 --rdg 47.7026983833543 --score-min L,4.77615534466375,2.00795144339831 --gbar 3 --mm --mp 3.49337565197466,1.08910369946333 --cp-ival 2 --local --trim3 8 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 766s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '2' because it was < 2 characters long 766s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '14' because it was < 2 characters long 766s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '16' because it was < 2 characters long 766s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 766s Warning: skipping mate #1 of read '17' because it was < 2 characters long 766s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '22' because it was < 2 characters long 766s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '23' because it was < 2 characters long 766s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 766s Warning: skipping mate #2 of read '26' because it was < 2 characters long 766s 36 reads; of these: 766s 24 (66.67%) were paired; of these: 766s 24 (100.00%) aligned concordantly 0 times 766s 0 (0.00%) aligned concordantly exactly 1 time 766s 0 (0.00%) aligned concordantly >1 times 766s ---- 766s 24 pairs aligned concordantly 0 times; of these: 766s 0 (0.00%) aligned discordantly 1 time 766s ---- 766s 24 pairs aligned 0 times concordantly or discordantly; of these: 766s 48 mates make up the pairs; of these: 766s 48 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 12 (33.33%) were unpaired; of these: 766s 12 (100.00%) aligned 0 times 766s 0 (0.00%) aligned exactly 1 time 766s 0 (0.00%) aligned >1 times 766s 0.00% overall alignment rate 766s Read 50 alignments... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 0 alignments, 0 edits 766s --------------- 766s PASSED 766s Flattened IUPAC characters 766s Mutating sequence Sim.pm.2 766s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutating sequence Sim.pm.1 766s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 766s Finished SNPs 766s Finished ref gaps 766s Finished read gaps 766s Mutated reference genome to subject genome 766s SNPs introduced: 5 766s Reference gaps introduced: 0 766s Read gaps introduced: 0 766s Rearrangements introduced: 0 766s Created read sampler 766s Sampling 35 reads 766s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 766s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 766s parsing sequence Sim.pm.1... 766s parsing sequence Sim.pm.2... 766s Parsed 74 reference bases 766s *** Run 12 of 100 766s /usr/bin/bowtie2 --cp-ival 1 -D 35 --mp 6.80100895189017,4.51514105907967 --rfg 4.35817249139988 --score-min L,3.25174041530021,8.90208524264267 --cp-min 16 --ma 29.4225670108191 --trim5 4 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 766s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '1' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 766s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '2' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 766s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '4' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '9' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 766s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '10' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 766s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '15' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 766s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '17' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 766s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '18' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 766s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '19' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 766s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 766s Warning: skipping read '25' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 766s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '26' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 766s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '29' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 766s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '30' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 766s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '31' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 766s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '33' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 766s 35 reads; of these: 766s 35 (100.00%) were unpaired; of these: 766s 32 (91.43%) aligned 0 times 766s 2 (5.71%) aligned exactly 1 time 766s 1 (2.86%) aligned >1 times 766s 8.57% overall alignment rate 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s /usr/bin/bowtie2 --cp-ival 1 -D 35 --mp 6.80100895189017,4.51514105907967 --rfg 4.35817249139988 --score-min L,3.25174041530021,8.90208524264267 --cp-min 16 --ma 29.4225670108191 --trim5 4 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 766s Processing line... 766s CT 766s CT 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s TTAC 766s TTAC 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s Processing line... 766s AACGCAGTTACCTCC 766s AACGCAGTTACCTCC 766s Processing line... 766s --- Summary --- 766s Read 1 reference strings 766s Checked 3 alignments, 0 edits 766s --------------- 766s PASSED 766s ALSO checking that bowtie2 and bowtie2-align match up 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 766s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '1' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 766s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '2' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 766s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '4' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '9' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 766s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '10' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 766s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '15' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 766s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '17' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 766s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '18' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 766s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '19' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 766s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 766s Warning: skipping read '25' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 766s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '26' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 766s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '29' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 766s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '30' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 766s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '31' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 766s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '33' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 766s 35 reads; of these: 766s 35 (100.00%) were unpaired; of these: 766s 32 (91.43%) aligned 0 times 766s 2 (5.71%) aligned exactly 1 time 766s 1 (2.86%) aligned >1 times 766s 8.57% overall alignment rate 766s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 766s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 766s /usr/bin/bowtie2 --cp-ival 1 -D 35 --mp 6.80100895189017,4.51514105907967 --rfg 4.35817249139988 --score-min L,3.25174041530021,8.90208524264267 --cp-min 16 --ma 29.4225670108191 --trim5 4 -q -p 4 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 766s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 766s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 766s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '1' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 766s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '2' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 766s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '4' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 766s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '9' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 766s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '10' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 766s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '15' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 766s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '17' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 766s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '18' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 766s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '19' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 766s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 766s Warning: skipping read '25' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 766s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '26' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 766s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '29' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 766s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '30' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 766s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '31' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 766s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 766s Warning: skipping read '33' because it was < 2 characters long 766s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 766s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 767s 35 reads; of these: 767s 35 (100.00%) were unpaired; of these: 767s 32 (91.43%) aligned 0 times 767s 2 (5.71%) aligned exactly 1 time 767s 1 (2.86%) aligned >1 times 767s 8.57% overall alignment rate 767s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.1 767s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.2 767s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 4 767s Reference gaps introduced: 0 767s Read gaps introduced: 0 767s Rearrangements introduced: 0 767s Created read sampler 767s Sampling 39 reads 767s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 767s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s Parsed 74 reference bases 767s *** Run 13 of 100 767s /usr/bin/bowtie2 --trim3 2 --nofw --mp 4.86266571671077,4.65266445860103 -N 1 -L26 --n-ceil 0.545366548866107,0.254105878108647 --cp-ival 1 --score-min L,2.57805810176532,6.94548710173294 --cp-min 6 -M 2 --np 1 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 767s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (1) 767s Warning: skipping mate #2 of read '1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 767s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 767s Warning: skipping mate #1 of read '14' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 767s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 767s Warning: skipping mate #1 of read '37' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 767s 39 reads; of these: 767s 37 (94.87%) were paired; of these: 767s 37 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 37 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 37 pairs aligned 0 times concordantly or discordantly; of these: 767s 74 mates make up the pairs; of these: 767s 68 (91.89%) aligned 0 times 767s 4 (5.41%) aligned exactly 1 time 767s 2 (2.70%) aligned >1 times 767s 2 (5.13%) were unpaired; of these: 767s 2 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 7.89% overall alignment rate 767s Read 50 alignments... 767s /usr/bin/bowtie2 --trim3 2 --nofw --mp 4.86266571671077,4.65266445860103 -N 1 -L26 --n-ceil 0.545366548866107,0.254105878108647 --cp-ival 1 --score-min L,2.57805810176532,6.94548710173294 --cp-min 6 -M 2 --np 1 -r -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s ACAACGCAGTTACCTCCTGAA 767s ACAACGCAGTTACCTCCTGAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s ACCGAGATAT 767s ACCGAGATAT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CA 767s CA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AACAACGC 767s AACAACGC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GCAGTTACCT 767s GCAGTTACCT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AG 767s AG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 6 alignments, 0 edits 767s --------------- 767s PASSED 767s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 767s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (1) 767s Warning: skipping mate #2 of read '1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 767s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 767s Warning: skipping mate #1 of read '14' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 767s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 767s Warning: skipping mate #1 of read '37' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 767s 39 reads; of these: 767s 37 (94.87%) were paired; of these: 767s 37 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 37 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 37 pairs aligned 0 times concordantly or discordantly; of these: 767s 74 mates make up the pairs; of these: 767s 68 (91.89%) aligned 0 times 767s 4 (5.41%) aligned exactly 1 time 767s 2 (2.70%) aligned >1 times 767s 2 (5.13%) were unpaired; of these: 767s 2 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 7.89% overall alignment rate 767s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 767s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 767s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 767s /usr/bin/bowtie2 --trim3 2 --nofw --mp 4.86266571671077,4.65266445860103 -N 1 -L26 --n-ceil 0.545366548866107,0.254105878108647 --cp-ival 1 --score-min L,2.57805810176532,6.94548710173294 --cp-min 6 -M 2 --np 1 -r -p 4 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 767s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 767s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 767s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 767s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (1) 767s Warning: skipping mate #2 of read '1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 767s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 767s Warning: skipping mate #1 of read '14' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 767s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 767s Warning: skipping mate #1 of read '37' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 767s 39 reads; of these: 767s 37 (94.87%) were paired; of these: 767s 37 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 37 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 37 pairs aligned 0 times concordantly or discordantly; of these: 767s 74 mates make up the pairs; of these: 767s 68 (91.89%) aligned 0 times 767s 4 (5.41%) aligned exactly 1 time 767s 2 (2.70%) aligned >1 times 767s 2 (5.13%) were unpaired; of these: 767s 2 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 7.89% overall alignment rate 767s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.1 767s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.2 767s Introducing 4 SNPs, 1/1 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 7 767s Reference gaps introduced: 1 767s Read gaps introduced: 1 767s Rearrangements introduced: 0 767s Created read sampler 767s Sampling 116 reads 767s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 767s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s Parsed 74 reference bases 767s *** Run 14 of 100 767s /usr/bin/bowtie2 --score-min L,3.43599676995525,4.53313291553236 --mm --cp-ival 1 --n-ceil 0.205654543349816,0.816946780514194 -D 5 --cp-min 6 --mp 9.5075173075958,2.57507280301358 --nofw --ma 36.959411782003 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 767s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '5' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '8' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 767s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '11' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 767s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '17' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 767s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '23' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 767s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '50' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 767s Read 50 alignments... 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 767s Read 100 alignments... 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 767s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '72' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 767s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '75' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 767s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '93' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 767s Read 150 alignments... 767s 116 Read 200 alignments... 767s reads; of these: 767s 116 (100.00%) were paired; of these: 767s 116 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 116 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 116 pairs aligned 0 times concordantly or discordantly; of these: 767s 232 mates make up the pairs; of these: 767s 197 (84.91%) aligned 0 times 767s 27 (11.64%) aligned exactly 1 time 767s 8 (3.45%) aligned >1 times 767s 15.09% overall alignment rate 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TGAA 767s TGAA 767s Processing line... 767s Processing line... 767s AACGCAGTTACCTCCTG 767s AACGCAGTTACCTCCTG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TACCTCCTGAAA 767s TACCTCCTGAAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TC 767s TC 767s Processing line... 767s Processing line... 767s AACAACGC 767s AACAACGC 767s Processing line... 767s Processing line... 767s ACG 767s ACG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TCCTGA 767s TCCTGA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CCTC 767s CCTC 767s Processing line... 767s Processing line... 767s AC 767s AC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AT 767s AT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CAGTTACCTCCTGAAAAC 767s CAGTTACCTCCTGAAAAC 767s Processing line... 767s Processing line... 767s GTC 767s GTC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CAACGCAGTTACCTCCTGAA 767s CAACGCAGTTACCTCCTGAA 767s Processing line... 767s Processing line... 767s TC 767s TC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AGTTACCTCCT 767s AGTTACCTCCT 767s Processing line... 767s Processing line... 767s CC 767s CC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TACC 767s TACC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TACCT 767s TACCT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CGCAGTT 767s CGCAGTT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AACATCC 767s AACATCC 767s Processing line... 767s Processing line... 767s TTACCTCCTGAAAACAT 767s TTACCTCCTGAAAACAT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CTGAA 767s CTGAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GCAGTTACCTCC 767s GCAGTTACCTCC 767s Processing line... 767s Processing line... 767s CGCAG 767s CGCAG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TCCTGAA 767s TCCTGAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TAAC 767s TAAC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s ACCTCCTGAAAACA 767s ACCTCCTGAAAACA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GTTACCTCCTGAAAACA 767s GTTACCTCCTGAAAACA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AA 767s AA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AACGCAGTTACCTCCTGAAA 767s AACGCAGTTACCTCCTGAAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CAACGCAGTTACCTCCTGAAAACA 767s CAACGCAGTTACCTCCTGAAAACA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TGAA 767s TGAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CTGAAAACAT 767s CTGAAAACAT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AACAACGCAGTTACCTCCTGAAAACATCC 767s AACAACGCAGTTACCTCCTGAAAACATCC 767s Processing line... 767s Processing line... 767s CAGTTAC 767s CAGTTAC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 35 alignments, 0 edits 767s --------------- 767s PASSED 767s ALSO checking that bowtie2 and bowtie2-align match up 767s /usr/bin/bowtie2 --score-min L,3.43599676995525,4.53313291553236 --mm --cp-ival 1 --n-ceil 0.205654543349816,0.816946780514194 -D 5 --cp-min 6 --mp 9.5075173075958,2.57507280301358 --nofw --ma 36.959411782003 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 767s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '5' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '8' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 767s Warning: skipping mate #2 of read '11' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '11' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 767s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '17' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 767s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '23' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 767s Warning: skipping mate #2 of read '50' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '50' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 767s Warning: skipping mate #2 of read '72' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '72' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 767s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '75' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 767s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (0) 767s Warning: skipping mate #2 of read '93' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 767s 116 reads; of these: 767s 116 (100.00%) were paired; of these: 767s 116 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 116 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 116 pairs aligned 0 times concordantly or discordantly; of these: 767s 232 mates make up the pairs; of these: 767s 197 (84.91%) aligned 0 times 767s 27 (11.64%) aligned exactly 1 time 767s 8 (3.45%) aligned >1 times 767s 15.09% overall alignment rate 767s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.2 767s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.1 767s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 9 767s Reference gaps introduced: 1 767s Read gaps introduced: 2 767s Rearrangements introduced: 0 767s Created read sampler 767s Sampling 148 reads 767s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 767s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s Parsed 74 reference bases 767s *** Run 15 of 100 767s /usr/bin/bowtie2 --rfg 12.4384028805719 --rdg 13.5696867808809 --score-min L,8.30945666521034,7.77807472792284 --mm --mp 9.55935313205469,3.83996941540269 --cp-ival 3 --local --np 2 --trim5 9 --cp-min 4 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '5' because it was < 2 characters long 767s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '6' because it was < 2 characters long 767s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '12' because it was < 2 characters long 767s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '16' because it was < 2 characters long 767s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '17' because it was < 2 characters long 767s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '23' because it was < 2 characters long 767s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '25' because it was < 2 characters long 767s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '31' because it was < 2 characters long 767s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '33' because it was < 2 characters long 767s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '42' because it was < 2 characters long 767s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '44' because it was < 2 characters long 767s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '52' because it was < 2 characters long 767s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '53' because it was < 2 characters long 767s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '57' because it was < 2 characters long 767s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '61' because it was < 2 characters long 767s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '65' because it was < 2 characters long 767s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '66' because it was < 2 characters long 767s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '67' because it was < 2 characters long 767s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '68' because it was < 2 characters long 767s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '69' because it was < 2 characters long 767s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '72' because it was < 2 characters long 767s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '76' because it was < 2 characters long 767s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '82' because it was < 2 characters long 767s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '83' because it was < 2 characters long 767s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '86' because it was < 2 characters long 767s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '87' because it was < 2 characters long 767s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '90' because it was < 2 characters long 767s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '91' because it was < 2 characters long 767s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '92' because it was < 2 characters long 767s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '93' because it was < 2 characters long 767s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '94' because it was < 2 characters long 767s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '98' because it was < 2 characters long 767s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '106' because it was < 2 characters long 767s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '107' because it was < 2 characters long 767s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '112' because it was < 2 characters long 767s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '117' because it was < 2 characters long 767s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '118' because it was < 2 characters long 767s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '121' because it was < 2 characters long 767s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '122' because it was < 2 characters long 767s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '124' because it was < 2 characters long 767s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '127' because it was < 2 characters long 767s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '129' because it was < 2 characters long 767s Warning: skipping read '132' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '132' because it was < 2 characters long 767s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '133' because it was < 2 characters long 767s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '135' because it was < 2 characters long 767s Warning: skipping read '141' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '141' because it was < 2 characters long 767s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '142' because it was < 2 characters long 767s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '144' because it was < 2 characters long 767s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '145' because it was < 2 characters long 767s 148 reads; of these: 767s 148 (100.00%) were unpaired; of these: 767s 148 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 0.00% overall alignment rate 767s Read 50 alignments... 767s Read 100 alignments... 767s Read 150 alignments... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s /usr/bin/bowtie2 --rfg 12.4384028805719 --rdg 13.5696867808809 --score-min L,8.30945666521034,7.77807472792284 --mm --mp 9.55935313205469,3.83996941540269 --cp-ival 3 --local --np 2 --trim5 9 --cp-min 4 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 0 alignments, 0 edits 767s --------------- 767s PASSED 767s ALSO checking that bowtie2 and bowtie2-align match up 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '5' because it was < 2 characters long 767s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '6' because it was < 2 characters long 767s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '12' because it was < 2 characters long 767s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '16' because it was < 2 characters long 767s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '17' because it was < 2 characters long 767s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '23' because it was < 2 characters long 767s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '25' because it was < 2 characters long 767s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '31' because it was < 2 characters long 767s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '33' because it was < 2 characters long 767s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '42' because it was < 2 characters long 767s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '44' because it was < 2 characters long 767s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '52' because it was < 2 characters long 767s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '53' because it was < 2 characters long 767s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '57' because it was < 2 characters long 767s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '61' because it was < 2 characters long 767s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '65' because it was < 2 characters long 767s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '66' because it was < 2 characters long 767s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '67' because it was < 2 characters long 767s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '68' because it was < 2 characters long 767s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '69' because it was < 2 characters long 767s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '72' because it was < 2 characters long 767s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '76' because it was < 2 characters long 767s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '82' because it was < 2 characters long 767s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '83' because it was < 2 characters long 767s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '86' because it was < 2 characters long 767s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '87' because it was < 2 characters long 767s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '90' because it was < 2 characters long 767s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '91' because it was < 2 characters long 767s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '92' because it was < 2 characters long 767s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '93' because it was < 2 characters long 767s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '94' because it was < 2 characters long 767s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '98' because it was < 2 characters long 767s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '106' because it was < 2 characters long 767s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '107' because it was < 2 characters long 767s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '112' because it was < 2 characters long 767s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '117' because it was < 2 characters long 767s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '118' because it was < 2 characters long 767s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '121' because it was < 2 characters long 767s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '122' because it was < 2 characters long 767s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '124' because it was < 2 characters long 767s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '127' because it was < 2 characters long 767s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '129' because it was < 2 characters long 767s Warning: skipping read '132' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '132' because it was < 2 characters long 767s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '133' because it was < 2 characters long 767s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '135' because it was < 2 characters long 767s Warning: skipping read '141' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '141' because it was < 2 characters long 767s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '142' because it was < 2 characters long 767s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '144' because it was < 2 characters long 767s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '145' because it was < 2 characters long 767s 148 reads; of these: 767s 148 (100.00%) were unpaired; of these: 767s 148 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 0.00% overall alignment rate 767s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 767s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 767s /usr/bin/bowtie2 --rfg 12.4384028805719 --rdg 13.5696867808809 --score-min L,8.30945666521034,7.77807472792284 --mm --mp 9.55935313205469,3.83996941540269 --cp-ival 3 --local --np 2 --trim5 9 --cp-min 4 -q -p 2 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '5' because it was < 2 characters long 767s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '6' because it was < 2 characters long 767s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '12' because it was < 2 characters long 767s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '16' because it was < 2 characters long 767s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '17' because it was < 2 characters long 767s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '23' because it was < 2 characters long 767s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '25' because it was < 2 characters long 767s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '31' because it was < 2 characters long 767s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '33' because it was < 2 characters long 767s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '42' because it was < 2 characters long 767s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '44' because it was < 2 characters long 767s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '52' because it was < 2 characters long 767s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '53' because it was < 2 characters long 767s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '57' because it was < 2 characters long 767s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '61' because it was < 2 characters long 767s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '65' because it was < 2 characters long 767s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '66' because it was < 2 characters long 767s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '67' because it was < 2 characters long 767s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '68' because it was < 2 characters long 767s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '69' because it was < 2 characters long 767s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '72' because it was < 2 characters long 767s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '76' because it was < 2 characters long 767s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '82' because it was < 2 characters long 767s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '83' because it was < 2 characters long 767s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '86' because it was < 2 characters long 767s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '87' because it was < 2 characters long 767s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '90' because it was < 2 characters long 767s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '91' because it was < 2 characters long 767s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '92' because it was < 2 characters long 767s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '93' because it was < 2 characters long 767s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '94' because it was < 2 characters long 767s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '98' because it was < 2 characters long 767s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '106' because it was < 2 characters long 767s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '107' because it was < 2 characters long 767s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '112' because it was < 2 characters long 767s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '117' because it was < 2 characters long 767s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '118' because it was < 2 characters long 767s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '121' because it was < 2 characters long 767s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '122' because it was < 2 characters long 767s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '124' because it was < 2 characters long 767s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '127' because it was < 2 characters long 767s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '129' because it was < 2 characters long 767s Warning: skipping read '132' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '132' because it was < 2 characters long 767s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '133' because it was < 2 characters long 767s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '135' because it was < 2 characters long 767s Warning: skipping read '141' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '141' because it was < 2 characters long 767s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '142' because it was < 2 characters long 767s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '144' because it was < 2 characters long 767s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '145' because it was < 2 characters long 767s 148 reads; of these: 767s 148 (100.00%) were unpaired; of these: 767s 148 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 0.00% overall alignment rate 767s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 767s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 767s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 767s /usr/bin/bowtie2 --rfg 12.4384028805719 --rdg 13.5696867808809 --score-min L,8.30945666521034,7.77807472792284 --mm --mp 9.55935313205469,3.83996941540269 --cp-ival 3 --local --np 2 --trim5 9 --cp-min 4 -q -p 2 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 767s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '5' because it was < 2 characters long 767s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '6' because it was < 2 characters long 767s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '12' because it was < 2 characters long 767s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '16' because it was < 2 characters long 767s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '17' because it was < 2 characters long 767s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '23' because it was < 2 characters long 767s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '25' because it was < 2 characters long 767s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '31' because it was < 2 characters long 767s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '33' because it was < 2 characters long 767s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '42' because it was < 2 characters long 767s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '44' because it was < 2 characters long 767s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '52' because it was < 2 characters long 767s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '53' because it was < 2 characters long 767s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '57' because it was < 2 characters long 767s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '61' because it was < 2 characters long 767s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '65' because it was < 2 characters long 767s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '66' because it was < 2 characters long 767s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '67' because it was < 2 characters long 767s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '68' because it was < 2 characters long 767s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '69' because it was < 2 characters long 767s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '72' because it was < 2 characters long 767s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '76' because it was < 2 characters long 767s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '82' because it was < 2 characters long 767s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '83' because it was < 2 characters long 767s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '86' because it was < 2 characters long 767s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '87' because it was < 2 characters long 767s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '90' because it was < 2 characters long 767s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '91' because it was < 2 characters long 767s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '92' because it was < 2 characters long 767s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '93' because it was < 2 characters long 767s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '94' because it was < 2 characters long 767s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '98' because it was < 2 characters long 767s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '106' because it was < 2 characters long 767s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '107' because it was < 2 characters long 767s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '112' because it was < 2 characters long 767s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '117' because it was < 2 characters long 767s Warning: skipping read '118' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '118' because it was < 2 characters long 767s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '121' because it was < 2 characters long 767s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '122' because it was < 2 characters long 767s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '124' because it was < 2 characters long 767s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '127' because it was < 2 characters long 767s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '129' because it was < 2 characters long 767s Warning: skipping read '132' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '132' because it was < 2 characters long 767s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '133' because it was < 2 characters long 767s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '135' because it was < 2 characters long 767s Warning: skipping read '141' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '141' because it was < 2 characters long 767s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 767s Warning: skipping read '142' because it was < 2 characters long 767s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '144' because it was < 2 characters long 767s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '145' because it was < 2 characters long 767s 148 reads; of these: 767s 148 (100.00%) were unpaired; of these: 767s 148 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 0.00% overall alignment rate 767s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.2 767s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.1 767s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 5 767s Reference gaps introduced: 1 767s Read gaps introduced: 0 767s Rearrangements introduced: 2 767s Created read sampler 767s Sampling 59 reads 767s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 767s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s *** Run 16 of 100 767s /usr/bin/bowtie2 -R 4 --trim3 2 --ma 11.0790437160613 --cp-ival 1 --cp-min 2 --trim5 7 --mm --score-min L,8.01193857799041,8.15317832493231 --np 11 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 767s Parsed 74 reference bases 767s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 767s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 767s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 767s 59 reads; of these: 767s 51 (86.44%) were paired; of these: 767s 50 (98.04%) aligned concordantly 0 times 767s 1 (1.96%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 50 pairs aligned concordantly 0 times; of these: 767s 1 (2.00%) aligned discordantly 1 time 767s ---- 767s 49 pairs aligned 0 times concordantly or discordantly; of these: 767s 98 mates make up the pairs; of these: 767s 79 (80.61%) aligned 0 times 767s 15 (15.31%) aligned exactly 1 time 767s 4 (4.08%) aligned >1 times 767s 8 (13.56%) were unpaired; of these: 767s 6 (75.00%) aligned 0 times 767s 1 (12.50%) aligned exactly 1 time 767s 1 (12.50%) aligned >1 times 767s 22.73% overall alignment rate 767s Read 50 alignments... 767s Read 100 alignments... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s ACGT 767s ACGT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CCTCC 767s CCTCC 767s Processing line... 767s Processing line... 767s ACAT 767s ACAT 767s Processing line... 767s Processing line... 767s TAC 767s TAC 767s Processing line... 767s AACAACGCAG 767s AACAACGCAG 767s Processing line... 767s AACAACGCAGTTACCT 767s AACAACGCAGTTACCT 767s Processing line... 767s TCCTGAAAACAT 767s TCCTGAAAACAT 767s Processing line... 767s GCAGTTACC 767s GCAGTTACC 767s Processing line... 767s Processing line... 767s ACATC 767s ACATC 767s Processing line... 767s Processing line... 767s AAC 767s AAC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CAGTTACCTCCTGAAAACAT 767s CAGTTACCTCCTGAAAACAT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GA 767s GA 767s Processing line... 767s Processing line... 767s Processing line... 767s CGCAGTTA 767s CGCAGTTA 767s Processing line... 767s Processing line... 767s AACA 767s AACA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GAGATATGAGTGATTAATAACGTCT 767s GAGATATGAGTGATTAATAACGTCT 767s Processing line... 767s Processing line... 767s AACAACGCAGTTACCTC 767s AACAACGCAGTTACCTC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CAACGCAGTTACCTCCT 767s CAACGCAGTTACCTCCT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s ACC 767s ACC 767s Processing line... 767s ACGCAGTT 767s ACGCAGTT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CAACGCAGTTACCT 767s CAACGCAGTTACCT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TCCTG 767s TCCTG 767s Processing line... 767s Processing line... 767s CAA 767s CAA 767s Processing line... 767s Processing line... 767s AACGCAG 767s AACGCAG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GTTACCTCCTGA 767s GTTACCTCCTGA 767s Processing line... 767s TACCTC 767s TACCTC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 25 alignments, 0 edits 767s --------------- 767s PASSED 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.2 767s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.1 767s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 5 767s Reference gaps introduced: 0 767s Read gaps introduced: 0 767s Rearrangements introduced: 1 767s Created read sampler 767s Sampling 21 reads 767s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 767s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s Parsed 74 reference bases 767s *** Run 17 of 100 767s /usr/bin/bowtie2 --score-min L,4.29500179229079,8.33508622109999 --rdg 3.83833062707358,14.2608418363014 --gbar 5 --trim3 1 -N 0 -L12 --cp-ival 1 --trim5 9 -k 2 --cp-min 5 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 767s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '5' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '13' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '15' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '18' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 767s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '20' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s 21 reads; of these: 767s 13 (61.90%) were paired; of these: 767s 13 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 13 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 13 pairs aligned 0 times concordantly or discordantly; of these: 767s 26 mates make up the pairs; of these: 767s 22 (84.62%) aligned 0 times 767s 4 (15.38%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 8 (38.10%) were unpaired; of these: 767s 8 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 11.76% overall alignment rate 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AACGCAGTTACCTCCTGAAAA 767s AACGCAGTTACCTCCTGAAAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AGTTACCTCCTGAAAA 767s AGTTACCTCCTGAAAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CCTCCTGAA 767s CCTCCTGAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CCTCCTGA 767s CCTCCTGA 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 4 alignments, 0 edits 767s --------------- 767s PASSED 767s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 767s /usr/bin/bowtie2 --score-min L,4.29500179229079,8.33508622109999 --rdg 3.83833062707358,14.2608418363014 --gbar 5 --trim3 1 -N 0 -L12 --cp-ival 1 --trim5 9 -k 2 --cp-min 5 -f -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 767s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '5' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '13' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '15' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '18' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 767s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '20' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 767s 21 reads; of these: 767s 13 (61.90%) were paired; of these: 767s 13 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 13 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 13 pairs aligned 0 times concordantly or discordantly; of these: 767s 26 mates make up the pairs; of these: 767s 22 (84.62%) aligned 0 times 767s 4 (15.38%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 8 (38.10%) were unpaired; of these: 767s 8 (100.00%) aligned 0 times 767s 0 (0.00%) aligned exactly 1 time 767s 0 (0.00%) aligned >1 times 767s 11.76% overall alignment rate 767s Flattened IUPAC characters 767s Mutating sequence Sim.pm.1 767s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutating sequence Sim.pm.2 767s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 767s Finished SNPs 767s Finished ref gaps 767s Finished read gaps 767s Mutated reference genome to subject genome 767s SNPs introduced: 1 767s Reference gaps introduced: 0 767s Read gaps introduced: 1 767s Rearrangements introduced: 0 767s Created read sampler 767s Sampling 60 reads 767s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 767s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 767s parsing sequence Sim.pm.1... 767s parsing sequence Sim.pm.2... 767s Parsed 74 reference bases 767s *** Run 18 of 100 767s /usr/bin/bowtie2 --np 6 --trim5 9 --cp-min 2 --ma 35.8041702193927 --gbar 3 --score-min L,4.45616629616084,3.93099969119531 --cp-ival 3 --n-ceil 1.14974640343732,1.0492703454513 --mp 7.13530155527435,5.4751968893184 --trim3 7 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 767s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 767s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 767s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '0' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 767s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '1' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 767s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '2' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 767s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '4' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 767s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '8' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 767s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '12' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 767s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '14' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 767s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '16' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 767s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '17' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 767s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '25' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 767s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '38' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 767s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '42' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 767s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '47' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 767s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 767s Warning: skipping read '52' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 767s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '58' because it was < 2 characters long 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 767s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 767s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 767s Warning: skipping mate #1 of read '59' because it was < 2 characters long 767s 60 reads; of these: 767s 43 (71.67%) were paired; of these: 767s 43 (100.00%) aligned concordantly 0 times 767s 0 (0.00%) aligned concordantly exactly 1 time 767s 0 (0.00%) aligned concordantly >1 times 767s ---- 767s 43 pairs aligned concordantly 0 times; of these: 767s 0 (0.00%) aligned discordantly 1 time 767s ---- 767s 43 pairs aligned 0 times concordantly or discordantly; of these: 767s 86 mates make up the pairs; of these: 767s 71 (82.56%) aligned 0 times 767s 9 (10.47%) aligned exactly 1 time 767s 6 (6.98%) aligned >1 times 767s 17 (28.33%) were unpaired; of these: 767s 15 (88.24%) aligned 0 times 767s 1 (5.88%) aligned exactly 1 time 767s 1 (5.88%) aligned >1 times 767s 16.50% overall alignment rate 767s Read 50 alignments... 767s Read 100 alignments... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CTCCTGAAAACATCC 767s CTCCTGAAAACATCC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CA 767s CA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TAACAACGCAGTTACC 767s TAACAACGCAGTTACC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AA 767s AA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GTTACCTCCT 767s GTTACCTCCT 767s Processing line... 767s Processing line... 767s AA 767s AA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s TATG 767s TATG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s ACCTCC 767s ACCTCC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CCTG 767s CCTG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s GCAG 767s GCAG 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CG 767s CG 767s Processing line... 767s ACGCAGTTACCTCC 767s ACGCAGTTACCTCC 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s CGA 767s CGA 767s Processing line... 767s CTCCTGAA 767s CTCCTGAA 767s Processing line... 767s Processing line... 767s Processing line... 767s AT 767s AT 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s AGA 767s AGA 767s Processing line... 767s TTACCTCCTGAA 767s TTACCTCCTGAA 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s Processing line... 767s --- Summary --- 767s Read 1 reference strings 767s Checked 17 alignments, 0 edits 767s --------------- 767s PASSED 767s ALSO checking that bowtie2 and bowtie2-align match up 767s /usr/bin/bowtie2 --np 6 --trim5 9 --cp-min 2 --ma 35.8041702193927 --gbar 3 --score-min L,4.45616629616084,3.93099969119531 --cp-ival 3 --n-ceil 1.14974640343732,1.0492703454513 --mp 7.13530155527435,5.4751968893184 --trim3 7 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 767s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 768s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 768s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '0' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 768s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '1' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 768s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '2' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 768s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '4' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 768s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '8' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 768s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '12' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 768s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '14' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 768s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '16' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 768s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '17' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 768s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '25' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 768s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '38' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 768s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '42' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 768s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '47' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 768s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '52' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 768s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '58' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 768s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '59' because it was < 2 characters long 768s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 768s 60 reads; of these: 768s 43 (71.67%) were paired; of these: 768s 43 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 43 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 43 pairs aligned 0 times concordantly or discordantly; of these: 768s 86 mates make up the pairs; of these: 768s 71 (82.56%) aligned 0 times 768s 9 (10.47%) aligned exactly 1 time 768s 6 (6.98%) aligned >1 times 768s 17 (28.33%) were unpaired; of these: 768s 15 (88.24%) aligned 0 times 768s 1 (5.88%) aligned exactly 1 time 768s 1 (5.88%) aligned >1 times 768s 16.50% overall alignment rate 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 6 SNPs, 0/3 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.1 768s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 7 768s Reference gaps introduced: 1 768s Read gaps introduced: 3 768s Rearrangements introduced: 0 768s Created read sampler 768s Sampling 69 reads 768s *** Run 19 of 100 768s /usr/bin/bowtie2 --trim5 7 -a --mm --rdg 34.3450000976795 --rfg 33.3998797913034,11.8628111948906 --score-min L,4.54374221349977,2.45461461955786 --trim3 6 -R 3 --cp-ival 1 --cp-min 7 -N 1 -L30 --mp 9.3384587731068,7.8560980203414 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 768s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 768s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 74 reference bases 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 768s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '5' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 768s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '9' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 768s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '18' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 768s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '20' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 768s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '26' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 768s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '28' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 768s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '35' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 768s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '38' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 768s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '42' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 768s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '43' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 768s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '45' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 768s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '46' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 768s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '49' because it was < 2 characters long 768s Warning: skipping mate #2 of read '49' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 768s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '51' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 768s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '63' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 768s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '64' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 768s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 768s Warning: skipping read '67' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 768s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '68' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 768s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 768s Warning: skipping mate #1 of read '69' because it was < 2 characters long 768s 69 reads; of these: 768s 54 (78.26%) were paired; of these: 768s 54 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 54 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 54 pairs aligned 0 times concordantly or discordantly; of these: 768s 108 mates make up the pairs; of these: 768s 104 (96.30%) aligned 0 times 768s 3 (2.78%) aligned exactly 1 time 768s 1 (0.93%) aligned >1 times 768s 15 (21.74%) were unpaired; of these: 768s 14 (93.33%) aligned 0 times 768s 1 (6.67%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 4.07% overall alignment rate 768s Read 50 alignments... 768s Read 100 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CCTGAAA 768s CCTGAAA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s AAAACATCC 768s AAAACATCC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s GTT 768s GTT 768s Processing line... 768s AAC 768s AAC 768s Processing line... 768s AAC 768s AAC 768s Processing line... 768s AAC 768s AAC 768s Processing line... 768s AAC 768s AAC 768s Processing line... 768s AAC 768s AAC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TCCT 768s TCCT 768s Processing line... 768s Processing line... 768s ACGCAGTTA 768s ACGCAGTTA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 10 alignments, 0 edits 768s --------------- 768s PASSED 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.1 768s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 5 768s Reference gaps introduced: 0 768s Read gaps introduced: 0 768s Rearrangements introduced: 2 768s Created read sampler 768s Sampling 80 reads 768s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 768s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 74 reference bases 768s *** Run 20 of 100 768s /usr/bin/bowtie2 -k 5 --norc --cp-min 2 --mm --rfg 11.5492087843282,6.2755059625106 --score-min L,3.95926532220913,2.4631413623537 --trim3 4 --mp 9.78923835236824,6.96624483127651 -N 0 -L13 -D 42 --cp-ival 1 --local -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 768s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '5' because it was < 2 characters long 768s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '11' because it was < 2 characters long 768s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '26' because it was < 2 characters long 768s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '41' because it was < 2 characters long 768s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '43' because it was < 2 characters long 768s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '45' because it was < 2 characters long 768s Warning: skipping mate #2 of read '48' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '48' because it was < 2 characters long 768s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '53' because it was < 2 characters long 768s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '76' because it was < 2 characters long 768s Warning: skipping mate #2 of read '76' because it was < 2 characters long 768s 80 reads; of these: 768s 72 (90.00%) were paired; of these: 768s 72 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 72 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 72 pairs aligned 0 times concordantly or discordantly; of these: 768s 144 mates make up the pairs; of these: 768s 144 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 8 (10.00%) were unpaired; of these: 768s 8 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s Read 50 alignments... 768s Read 100 alignments... 768s Read 150 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 0 alignments, 0 edits 768s --------------- 768s PASSED 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 2 SNPs, 4/1 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.1 768s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 5 768s Reference gaps introduced: 4 768s Read gaps introduced: 1 768s Rearrangements introduced: 0 768s Created read sampler 768s Sampling 23 reads 768s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 768s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 74 reference bases 768s *** Run 21 of 100 768s /usr/bin/bowtie2 --ma 29.8809385271183 --cp-ival 1 --n-ceil 1.0468913754382,0.218330361907408 --cp-min 2 --rfg 16.8498606464072,16.3110244243578 --norc --score-min L,1.90201459763164,9.83901967169562 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 768s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 768s 23 reads; of these: 768s 23 (100.00%) were paired; of these: 768s 23 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 23 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 23 pairs aligned 0 times concordantly or discordantly; of these: 768s 46 mates make up the pairs; of these: 768s 43 (93.48%) aligned 0 times 768s 2 (4.35%) aligned exactly 1 time 768s 1 (2.17%) aligned >1 times 768s 6.52% overall alignment rate 768s Read 50 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CT 768s CT 768s Processing line... 768s Processing line... 768s /usr/bin/bowtie2 --ma 29.8809385271183 --cp-ival 1 --n-ceil 1.0468913754382,0.218330361907408 --cp-min 2 --rfg 16.8498606464072,16.3110244243578 --norc --score-min L,1.90201459763164,9.83901967169562 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s AAAA 768s AAAA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s ATC 768s ATC 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 3 alignments, 0 edits 768s --------------- 768s PASSED 768s ALSO checking that bowtie2 and bowtie2-align match up 768s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 768s 23 reads; of these: 768s 23 (100.00%) were paired; of these: 768s 23 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 23 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 23 pairs aligned 0 times concordantly or discordantly; of these: 768s 46 mates make up the pairs; of these: 768s 43 (93.48%) aligned 0 times 768s 2 (4.35%) aligned exactly 1 time 768s 1 (2.17%) aligned >1 times 768s 6.52% overall alignment rate 768s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s *** Run 22 of 100 768s /usr/bin/bowtie2 --cp-min 3 --np 1 --trim3 9 --mp 2.78476566574773,2.57009826063102 --local --cp-ival 1 --n-ceil 0.045444769720922,1.10694092260207 --score-min L,6.05434800713304,4.06222203247662 --rfg 3.62700002980186,17.3948723210786 --gbar 3 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 768s Mutating sequence Sim.pm.1 768s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 2 768s Reference gaps introduced: 0 768s Read gaps introduced: 1 768s Rearrangements introduced: 1 768s Created read sampler 768s Sampling 62 reads 768s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 768s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 74 reference bases 768s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '2' because it was < 2 characters long 768s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '5' because it was < 2 characters long 768s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '7' because it was < 2 characters long 768s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '8' because it was < 2 characters long 768s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '10' because it was < 2 characters long 768s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '11' because it was < 2 characters long 768s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '14' because it was < 2 characters long 768s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '17' because it was < 2 characters long 768s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '27' because it was < 2 characters long 768s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '29' because it was < 2 characters long 768s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '30' because it was < 2 characters long 768s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '35' because it was < 2 characters long 768s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '37' because it was < 2 characters long 768s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '45' because it was < 2 characters long 768s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '47' because it was < 2 characters long 768s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '48' because it was < 2 characters long 768s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '52' because it was < 2 characters long 768s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '53' because it was < 2 characters long 768s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '56' because it was < 2 characters long 768s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '59' because it was < 2 characters long 768s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '60' because it was < 2 characters long 768s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '61' because it was < 2 characters long 768s 62 reads; of these: 768s 62 (100.00%) were unpaired; of these: 768s 62 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s Read 50 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s /usr/bin/bowtie2 --cp-min 3 --np 1 --trim3 9 --mp 2.78476566574773,2.57009826063102 --local --cp-ival 1 --n-ceil 0.045444769720922,1.10694092260207 --score-min L,6.05434800713304,4.06222203247662 --rfg 3.62700002980186,17.3948723210786 --gbar 3 -q -p 2 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 0 alignments, 0 edits 768s --------------- 768s PASSED 768s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 768s Warning: skipping read '2' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '2' because it was < 2 characters long 768s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '5' because it was < 2 characters long 768s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '7' because it was < 2 characters long 768s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '8' because it was < 2 characters long 768s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '10' because it was < 2 characters long 768s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '11' because it was < 2 characters long 768s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '14' because it was < 2 characters long 768s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '17' because it was < 2 characters long 768s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '27' because it was < 2 characters long 768s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '29' because it was < 2 characters long 768s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '30' because it was < 2 characters long 768s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '35' because it was < 2 characters long 768s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '37' because it was < 2 characters long 768s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '45' because it was < 2 characters long 768s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '47' because it was < 2 characters long 768s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '48' because it was < 2 characters long 768s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '52' because it was < 2 characters long 768s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '53' because it was < 2 characters long 768s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '56' because it was < 2 characters long 768s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '59' because it was < 2 characters long 768s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '60' because it was < 2 characters long 768s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '61' because it was < 2 characters long 768s 62 reads; of these: 768s 62 (100.00%) were unpaired; of these: 768s 62 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 768s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 768s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.1 768s Introducing 12 SNPs, 0/0 ref/read gaps, and 1 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 12 768s Reference gaps introduced: 1 768s Read gaps introduced: 0 768s Rearrangements introduced: 1 768s Created read sampler 768s Sampling 66 reads 768s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 768s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 74 reference bases 768s *** Run 23 of 100 768s /usr/bin/bowtie2 --cp-min 3 --np 1 -M 5 --trim5 5 --mp 4.05522678079748,2.92760061884581 --nofw -D 34 --cp-ival 1 --local --n-ceil 0.183888950678781,0.100858409690189 --trim3 8 --rdg 42.3446570538431,8.6736293706384 --rfg 49.7508933878625 --score-min L,6.81518419659262,8.7926801244625 --mm -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 768s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 768s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '1' because it was < 2 characters long 768s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '2' because it was < 2 characters long 768s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '3' because it was < 2 characters long 768s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '5' because it was < 2 characters long 768s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '6' because it was < 2 characters long 768s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '7' because it was < 2 characters long 768s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '9' because it was < 2 characters long 768s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '11' because it was < 2 characters long 768s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '12' because it was < 2 characters long 768s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '18' because it was < 2 characters long 768s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '23' because it was < 2 characters long 768s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '25' because it was < 2 characters long 768s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '26' because it was < 2 characters long 768s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '27' because it was < 2 characters long 768s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '30' because it was < 2 characters long 768s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '31' because it was < 2 characters long 768s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '33' because it was < 2 characters long 768s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '38' because it was < 2 characters long 768s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '39' because it was < 2 characters long 768s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '45' because it was < 2 characters long 768s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '48' because it was < 2 characters long 768s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '51' because it was < 2 characters long 768s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '55' because it was < 2 characters long 768s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '56' because it was < 2 characters long 768s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '57' because it was < 2 characters long 768s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '59' because it was < 2 characters long 768s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '61' because it was < 2 characters long 768s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '64' because it was < 2 characters long 768s 66 reads; of these: 768s 66 (100.00%) were unpaired; of these: 768s 66 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s Read 50 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s /usr/bin/bowtie2 --cp-min 3 --np 1 -M 5 --trim5 5 --mp 4.05522678079748,2.92760061884581 --nofw -D 34 --cp-ival 1 --local --n-ceil 0.183888950678781,0.100858409690189 --trim3 8 --rdg 42.3446570538431,8.6736293706384 --rfg 49.7508933878625 --score-min L,6.81518419659262,8.7926801244625 --mm -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 768s --- Summary --- 768s Read 1 reference strings 768s Checked 0 alignments, 0 edits 768s --------------- 768s PASSED 768s ALSO checking that bowtie2 and bowtie2-align match up 768s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 768s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '1' because it was < 2 characters long 768s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '2' because it was < 2 characters long 768s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '3' because it was < 2 characters long 768s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '5' because it was < 2 characters long 768s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '6' because it was < 2 characters long 768s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '7' because it was < 2 characters long 768s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '9' because it was < 2 characters long 768s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '11' because it was < 2 characters long 768s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '12' because it was < 2 characters long 768s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '18' because it was < 2 characters long 768s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '23' because it was < 2 characters long 768s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '25' because it was < 2 characters long 768s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '26' because it was < 2 characters long 768s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '27' because it was < 2 characters long 768s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '30' because it was < 2 characters long 768s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '31' because it was < 2 characters long 768s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '33' because it was < 2 characters long 768s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '38' because it was < 2 characters long 768s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '39' because it was < 2 characters long 768s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '45' because it was < 2 characters long 768s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '48' because it was < 2 characters long 768s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '51' because it was < 2 characters long 768s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '55' because it was < 2 characters long 768s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '56' because it was < 2 characters long 768s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '57' because it was < 2 characters long 768s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '59' because it was < 2 characters long 768s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '61' because it was < 2 characters long 768s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '64' because it was < 2 characters long 768s 66 reads; of these: 768s 66 (100.00%) were unpaired; of these: 768s 66 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 768s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 768s /usr/bin/bowtie2 --cp-min 3 --np 1 -M 5 --trim5 5 --mp 4.05522678079748,2.92760061884581 --nofw -D 34 --cp-ival 1 --local --n-ceil 0.183888950678781,0.100858409690189 --trim3 8 --rdg 42.3446570538431,8.6736293706384 --rfg 49.7508933878625 --score-min L,6.81518419659262,8.7926801244625 --mm -f -p 3 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 768s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 768s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '1' because it was < 2 characters long 768s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '2' because it was < 2 characters long 768s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '3' because it was < 2 characters long 768s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '5' because it was < 2 characters long 768s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '6' because it was < 2 characters long 768s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '7' because it was < 2 characters long 768s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '9' because it was < 2 characters long 768s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 768s Warning: skipping read '11' because it was < 2 characters long 768s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '12' because it was < 2 characters long 768s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '18' because it was < 2 characters long 768s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '23' because it was < 2 characters long 768s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '25' because it was < 2 characters long 768s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '26' because it was < 2 characters long 768s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '27' because it was < 2 characters long 768s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '30' because it was < 2 characters long 768s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '31' because it was < 2 characters long 768s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '33' because it was < 2 characters long 768s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '38' because it was < 2 characters long 768s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '39' because it was < 2 characters long 768s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '45' because it was < 2 characters long 768s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '48' because it was < 2 characters long 768s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '51' because it was < 2 characters long 768s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '55' because it was < 2 characters long 768s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '56' because it was < 2 characters long 768s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '57' because it was < 2 characters long 768s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '59' because it was < 2 characters long 768s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '61' because it was < 2 characters long 768s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '64' because it was < 2 characters long 768s 66 reads; of these: 768s 66 (100.00%) were unpaired; of these: 768s 66 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 768s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.1 768s Introducing 2 SNPs, 0/2 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 2 768s Reference gaps introduced: 0 768s Read gaps introduced: 2 768s Rearrangements introduced: 1 768s Created read sampler 768s Sampling 79 reads 768s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 768s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 74 reference bases 768s *** Run 24 of 100 768s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 0.712773950344783,1.48281435623729 --trim3 9 --rdg 19.9710527893805,17.1689088779303 --score-min L,2.10141796135368,4.68409572082951 --gbar 3 --mm --ma 11.6033302770383 --cp-min 3 --np 2 -k 3 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 768s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 768s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '1' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 768s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '3' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 768s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '5' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 768s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '6' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 768s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '7' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 768s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '10' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 768s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '12' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 768s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '14' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 768s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '26' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 768s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '29' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 768s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '33' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 768s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '34' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 768s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '36' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 768s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '46' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 768s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '60' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 768s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '61' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 768s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '62' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 768s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '64' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 768s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '66' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 768s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '76' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 768s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '79' because it was < 2 characters long 768s 79 reads; of these: 768s 63 (79.75%) were paired; of these: 768s 63 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 63 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 63 pairs aligned 0 times concordantly or discordantly; of these: 768s 126 mates make up the pairs; of these: 768s 110 (87.30%) aligned 0 times 768s 14 (11.11%) aligned exactly 1 time 768s 2 (1.59%) aligned >1 times 768s 16 (20.25%) were unpaired; of these: 768s 12 (75.00%) aligned 0 times 768s 4 (25.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 14.08% overall alignment rate 768s Read 50 alignments... 768s Read 100 alignments... 768s Read 150 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s AGTTACCTCC 768s AGTTACCTCC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TAACAACGCAGTTACCT 768s TAACAACGCAGTTACCT 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s GTTACCTCCTG 768s GTTACCTCCTG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CATCC 768s CATCC 768s Processing line... 768s CCTCCTGAA 768s CCTCCTGAA 768s Processing line... 768s Processing line... 768s CAACGCAG 768s CAACGCAG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CTGAAAACATCC 768s CTGAAAACATCC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CT 768s CT 768s Processing line... 768s CT 768s CT 768s Processing line... 768s CT 768s CT 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s ACGCAGTTACCTCC 768s ACGCAGTTACCTCC 768s Processing line... 768s Processing line... 768s AACAACGCAG 768s AACAACGCAG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s AACAAC 768s AACAAC 768s Processing line... 768s Processing line... 768s CAGTTACCTCCTGAAA 768s CAGTTACCTCCTGAAA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TGAAAACAT 768s TGAAAACAT 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TACCTCCTGAA 768s TACCTCCTGAA 768s Processing line... 768s Processing line... 768s Processing line... 768s CGCAGT 768s CGCAGT 768s Processing line... 768s Processing line... 768s GAAAACA 768s GAAAACA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s ACCTCCTGAA 768s ACCTCCTGAA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s AGATA 768s AGATA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TTA 768s TTA 768s Processing line... 768s TAA 768s TAA 768s Processing line... 768s TTA 768s TTA 768s Processing line... 768s CGCAGTTACC 768s CGCAGTTACC 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 24 alignments, 0 edits 768s --------------- 768s PASSED 768s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 768s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 0.712773950344783,1.48281435623729 --trim3 9 --rdg 19.9710527893805,17.1689088779303 --score-min L,2.10141796135368,4.68409572082951 --gbar 3 --mm --ma 11.6033302770383 --cp-min 3 --np 2 -k 3 -q -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 768s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 768s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '1' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 768s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '3' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 768s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '5' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 768s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '6' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 768s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '7' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 768s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '10' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 768s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '12' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 768s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '14' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 768s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '26' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 768s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '29' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 768s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '33' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 768s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '34' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 768s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '36' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 768s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '46' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 768s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '60' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 768s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '61' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 768s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '62' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 768s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '64' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 768s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '66' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 768s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 768s Warning: skipping read '76' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 768s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '79' because it was < 2 characters long 768s 79 reads; of these: 768s 63 (79.75%) were paired; of these: 768s 63 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 63 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 63 pairs aligned 0 times concordantly or discordantly; of these: 768s 126 mates make up the pairs; of these: 768s 110 (87.30%) aligned 0 times 768s 14 (11.11%) aligned exactly 1 time 768s 2 (1.59%) aligned >1 times 768s 16 (20.25%) were unpaired; of these: 768s 12 (75.00%) aligned 0 times 768s 4 (25.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 14.08% overall alignment rate 768s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.1 768s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.2 768s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 3 768s Reference gaps introduced: 0 768s Read gaps introduced: 1 768s Rearrangements introduced: 0 768s Created read sampler 768s Sampling 65 reads 768s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 768s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 768s *** Run 25 of 100 768s /usr/bin/bowtie2 --mm -i S,0.979431259563033 --score-min L,3.82515837817381,1.94314504236324 --rfg 34.4290650726625 --norc --ma 28.7304856563412 --cp-min 4 --cp-ival 2 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s Parsed 74 reference bases 768s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 768s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '5' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 768s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #1 of read '31' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 768s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 768s Warning: skipping mate #2 of read '49' because it was < 2 characters long 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 768s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 768s Read 50 alignments... 768s 65 reads; of these: 768s 65 (100.00%) were paired; of these: 768s 65 (100.00%) aligned concordantly 0 times 768s 0 (0.00%) aligned concordantly exactly 1 time 768s 0 (0.00%) aligned concordantly >1 times 768s ---- 768s 65 pairs aligned concordantly 0 times; of these: 768s 0 (0.00%) aligned discordantly 1 time 768s ---- 768s 65 pairs aligned 0 times concordantly or discordantly; of these: 768s 130 mates make up the pairs; of these: 768s 112 (86.15%) aligned 0 times 768s 13 (10.00%) aligned exactly 1 time 768s 5 (3.85%) aligned >1 times 768s 13.85% overall alignment rate 768s Read 100 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s AACAA 768s AACAA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s ACA 768s ACA 768s Processing line... 768s Processing line... 768s ACG 768s ACG 768s Processing line... 768s Processing line... 768s ACAACGCAGTTAC 768s ACAACGCAGTTAC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TAGA 768s TAGA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CGCAGTTACCTCCTG 768s CGCAGTTACCTCCTG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TAGACGAC 768s TAGACGAC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s ACCGAGATATGAGTGATTAATAACGT 768s ACCGAGATATGAGTGATTAATAACGT 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CTC 768s CTC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s ATG 768s ATG 768s Processing line... 768s Processing line... 768s TAACAACGCAGTTAC 768s TAACAACGCAGTTAC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TAACAACGCAGTTACC 768s TAACAACGCAGTTACC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s AC 768s AC 768s Processing line... 768s Processing line... 768s TAAC 768s TAAC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s GCA 768s GCA 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s AACGCAGTTACCTCCTG 768s AACGCAGTTACCTCCTG 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s TC 768s TC 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s CTCCTGAAAACAT 768s CTCCTGAAAACAT 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 18 alignments, 0 edits 768s --------------- 768s PASSED 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.1 768s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutating sequence Sim.pm.2 768s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 768s Finished SNPs 768s Finished ref gaps 768s Finished read gaps 768s Mutated reference genome to subject genome 768s SNPs introduced: 6 768s Reference gaps introduced: 0 768s Read gaps introduced: 0 768s Rearrangements introduced: 1 768s Created read sampler 768s Sampling 82 reads 768s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 768s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 768s parsing sequence Sim.pm.1... 768s parsing sequence Sim.pm.2... 768s *** Run 26 of 100 768s /usr/bin/bowtie2 --np 1 --score-min L,1.85180513905521,6.16130761276518 --cp-ival 1 --local -D 2 --cp-min 8 -N 1 -L30 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 768s Parsed 74 reference bases 768s Warning: skipping read '10' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '10' because it was < 2 characters long 768s Warning: skipping read '14' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '14' because it was < 2 characters long 768s Warning: skipping read '41' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '41' because it was < 2 characters long 768s Warning: skipping read '52' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '52' because it was < 2 characters long 768s Warning: skipping read '63' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '63' because it was < 2 characters long 768s Warning: skipping read '69' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '69' because it was < 2 characters long 768s Warning: skipping read '75' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '75' because it was < 2 characters long 768s 82 reads; of these: 768s 82 (100.00%) were unpaired; of these: 768s 82 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s Read 50 alignments... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s Processing line... 768s --- Summary --- 768s Read 1 reference strings 768s Checked 0 alignments, 0 edits 768s --------------- 768s PASSED 768s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 768s /usr/bin/bowtie2 --np 1 --score-min L,1.85180513905521,6.16130761276518 --cp-ival 1 --local -D 2 --cp-min 8 -N 1 -L30 -q -p 4 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 768s Warning: skipping read '10' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '10' because it was < 2 characters long 768s Warning: skipping read '14' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '14' because it was < 2 characters long 768s Warning: skipping read '41' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '41' because it was < 2 characters long 768s Warning: skipping read '52' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '52' because it was < 2 characters long 768s Warning: skipping read '63' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '63' because it was < 2 characters long 768s Warning: skipping read '69' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '69' because it was < 2 characters long 768s Warning: skipping read '75' because length (1) <= # seed mismatches (1) 768s Warning: skipping read '75' because it was < 2 characters long 768s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 768s 82 reads; of these: 768s 82 (100.00%) were unpaired; of these: 768s 82 (100.00%) aligned 0 times 768s 0 (0.00%) aligned exactly 1 time 768s 0 (0.00%) aligned >1 times 768s 0.00% overall alignment rate 768s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 768s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 768s Flattened IUPAC characters 768s Mutating sequence Sim.pm.2 769s *** Run 27 of 100 769s /usr/bin/bowtie2 --local --cp-ival 1 -D 9 --n-ceil 0.946968490952776,0.0963703690522729 --rfg 28.388501591991 --score-min L,9.67723521709675,9.54625150022627 -a --cp-min 4 --trim5 9 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 769s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.1 769s Introducing 0 SNPs, 2/0 ref/read gaps, and 1 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 3 769s Reference gaps introduced: 2 769s Read gaps introduced: 0 769s Rearrangements introduced: 1 769s Created read sampler 769s Sampling 45 reads 769s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 769s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 769s parsing sequence Sim.pm.1... 769s parsing sequence Sim.pm.2... 769s Parsed 74 reference bases 769s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '4' because it was < 2 characters long 769s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '6' because it was < 2 characters long 769s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '11' because it was < 2 characters long 769s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '14' because it was < 2 characters long 769s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '23' because it was < 2 characters long 769s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '25' because it was < 2 characters long 769s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '29' because it was < 2 characters long 769s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '32' because it was < 2 characters long 769s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '35' because it was < 2 characters long 769s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '43' because it was < 2 characters long 769s 45 reads; of these: 769s 38 (84.44%) were paired; of these: 769s 38 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 38 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 38 pairs aligned 0 times concordantly or discordantly; of these: 769s 76 mates make up the pairs; of these: 769s 76 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 7 (15.56%) were unpaired; of these: 769s 7 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s Read 50 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 0 alignments, 0 edits 769s --------------- 769s PASSED 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.2 769s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.1 769s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 9 769s Reference gaps introduced: 0 769s Read gaps introduced: 2 769s Rearrangements introduced: 0 769s Created read sampler 769s Sampling 118 reads 769s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 769s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 769s parsing sequence Sim.pm.1... 769s *** Run 28 of 100 769s /usr/bin/bowtie2 --mp 4.26172244606838,1.49258177907646 -N 0 --cp-ival 2 -a --score-min L,5.77238804039219,5.92012938680639 --rdg 30.5180302597734 --rfg 25.3597447148423,14.0860673949661 --cp-min 7 --trim5 1 --norc -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 769s parsing sequence Sim.pm.2... 769s Parsed 74 reference bases 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 769s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '17' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 769s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '55' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 769s Read 50 alignments... 769s Read 100 alignments... 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 769s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '78' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 769s Warning: skipping mate #2 of read '86' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '86' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 769s Warning: skipping mate #2 of read '93' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '93' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 769s Warning: skipping mate #2 of read '106' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '106' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 769s Read 150 alignments... 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 769s Read 200 alignments... 769s 118 reads; of these: 769s 116 (98.31%) were paired; of these: 769s 116 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 116 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 116 pairs aligned 0 times concordantly or discordantly; of these: 769s 232 mates make up the pairs; of these: 769s 219 (94.40%) aligned 0 times 769s 8 (3.45%) aligned exactly 1 time 769s 5 (2.16%) aligned >1 times 769s 2 (1.69%) were unpaired; of these: 769s 2 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 5.56% overall alignment rate 769s Read 250 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CAT 769s CAT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s TT 769s TT 769s Processing line... 769s TT 769s TT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s TG 769s TG 769s Processing line... 769s TG 769s TG 769s Processing line... 769s TG 769s TG 769s Processing line... 769s TG 769s TG 769s Processing line... 769s AACAACGCAGTT 769s AACAACGCAGTT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s ACGCA 769s ACGCA 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s AT 769s AT 769s Processing line... 769s AT 769s AT 769s Processing line... 769s AT 769s AT 769s Processing line... 769s AT 769s AT 769s Processing line... 769s AT 769s AT 769s Processing line... 769s AT 769s AT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CAACGCAGTTACCTCCTG 769s CAACGCAGTTACCTCCTG 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GC 769s GC 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CA 769s CA 769s Processing line... 769s CA 769s CA 769s Processing line... 769s CA 769s CA 769s Processing line... 769s CA 769s CA 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s GAGT 769s GAGT 769s Processing line... 769s Processing line... 769s GA 769s GA 769s Processing line... 769s GA 769s GA 769s Processing line... 769s GA 769s GA 769s Processing line... 769s GA 769s GA 769s Processing line... 769s GA 769s GA 769s Processing line... 769s GA 769s GA 769s Processing line... 769s GA 769s GA 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s TCT 769s TCT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s CAACGCAGTTACCTCCTGAAAACAT 769s CAACGCAGTTACCTCCTGAAAACAT 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 31 alignments, 0 edits 769s --------------- 769s PASSED 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.1 769s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.2 769s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 0 769s Reference gaps introduced: 0 769s Read gaps introduced: 1 769s Rearrangements introduced: 0 769s Created read sampler 769s Sampling 97 reads 769s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 769s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 769s parsing sequence Sim.pm.1... 769s parsing sequence Sim.pm.2... 769s Parsed 74 reference bases 769s *** Run 29 of 100 769s /usr/bin/bowtie2 --trim5 2 --norc --cp-min 3 --ma 28.6833760017003 -a --mm --score-min L,4.58905127601203,9.58722261335418 --rdg 1.72513707570576 --rfg 36.3725192712919 --cp-ival 2 --nofw --mp 6.49506149025645,6.30082616515934 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 769s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 769s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 769s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '7' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 769s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '11' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 769s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '18' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 769s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '21' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 769s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '23' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 769s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '29' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 769s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '37' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 769s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '42' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 769s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '54' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 769s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '56' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 769s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '57' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 769s Warning: skipping read '76' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '76' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 769s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '77' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 769s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '78' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 769s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '82' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 769s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '84' because it was < 2 characters long 769s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 769s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 769s 97 reads; of these: 769s 97 (100.00%) were unpaired; of these: 769s 97 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s Read 50 alignments... 769s Read 100 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 0 alignments, 0 edits 769s --------------- 769s PASSED 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.1 769s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.2 769s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 4 769s Reference gaps introduced: 0 769s Read gaps introduced: 0 769s Rearrangements introduced: 2 769s Created read sampler 769s Sampling 54 reads 769s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 769s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 769s parsing sequence Sim.pm.1... 769s parsing sequence Sim.pm.2... 769s *** Run 30 of 100 769s /usr/bin/bowtie2 --cp-min 3 --trim5 2 -i C,2.95315253130066 --np 1 --cp-ival 1 --local -a --score-min L,6.01546161170781,5.38504310917513 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 769s Parsed 74 reference bases 769s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '18' because it was < 2 characters long 769s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '28' because it was < 2 characters long 769s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '30' because it was < 2 characters long 769s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '47' because it was < 2 characters long 769s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '50' because it was < 2 characters long 769s 54 reads; of these: 769s 52 (96.30%) were paired; of these: 769s 52 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 52 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 52 pairs aligned 0 times concordantly or discordantly; of these: 769s 104 mates make up the pairs; of these: 769s 104 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 2 (3.70%) were unpaired; of these: 769s 2 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s Read 50 alignments... 769s Read 100 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 0 alignments, 0 edits 769s --------------- 769s PASSED 769s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 769s /usr/bin/bowtie2 --cp-min 3 --trim5 2 -i C,2.95315253130066 --np 1 --cp-ival 1 --local -a --score-min L,6.01546161170781,5.38504310917513 -f -p 4 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 769s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '18' because it was < 2 characters long 769s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '28' because it was < 2 characters long 769s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '30' because it was < 2 characters long 769s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '47' because it was < 2 characters long 769s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '50' because it was < 2 characters long 769s 54 reads; of these: 769s 52 (96.30%) were paired; of these: 769s 52 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 52 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 52 pairs aligned 0 times concordantly or discordantly; of these: 769s 104 mates make up the pairs; of these: 769s 104 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 2 (3.70%) were unpaired; of these: 769s 2 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 769s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 769s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 769s /usr/bin/bowtie2 --cp-min 3 --trim5 2 -i C,2.95315253130066 --np 1 --cp-ival 1 --local -a --score-min L,6.01546161170781,5.38504310917513 -f -p 4 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 769s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 769s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '18' because it was < 2 characters long 769s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '28' because it was < 2 characters long 769s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '30' because it was < 2 characters long 769s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '47' because it was < 2 characters long 769s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '50' because it was < 2 characters long 769s 54 reads; of these: 769s 52 (96.30%) were paired; of these: 769s 52 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 52 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 52 pairs aligned 0 times concordantly or discordantly; of these: 769s 104 mates make up the pairs; of these: 769s 104 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 2 (3.70%) were unpaired; of these: 769s 2 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.1 769s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.2 769s Introducing 8 SNPs, 1/3 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 8 769s Reference gaps introduced: 2 769s Read gaps introduced: 3 769s Rearrangements introduced: 0 769s Created read sampler 769s Sampling 124 reads 769s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 769s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 769s parsing sequence Sim.pm.1... 769s parsing sequence Sim.pm.2... 769s Parsed 74 reference bases 769s *** Run 31 of 100 769s /usr/bin/bowtie2 --cp-min 8 --local --cp-ival 4 --n-ceil 1.47818745190554,0.0409314324982333 --gbar 3 --score-min L,1.22764175354948,2.54147222453036 --rfg 27.2535869179083,10.8394183280648 -a --trim5 9 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 769s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '4' because it was < 2 characters long 769s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '12' because it was < 2 characters long 769s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '19' because it was < 2 characters long 769s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '33' because it was < 2 characters long 769s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '38' because it was < 2 characters long 769s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '42' because it was < 2 characters long 769s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '43' because it was < 2 characters long 769s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '52' because it was < 2 characters long 769s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '59' because it was < 2 characters long 769s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '63' because it was < 2 characters long 769s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '76' because it was < 2 characters long 769s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '77' because it was < 2 characters long 769s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '82' because it was < 2 characters long 769s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '83' because it was < 2 characters long 769s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '87' because it was < 2 characters long 769s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '90' because it was < 2 characters long 769s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '94' because it was < 2 characters long 769s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '103' because it was < 2 characters long 769s Warning: skipping mate #2 of read '111' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '111' because it was < 2 characters long 769s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '113' because it was < 2 characters long 769s Warning: skipping mate #1 of read '121' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '121' because it was < 2 characters long 769s Read 50 alignments... 769s 124 reads; of these: 769s 103 (83.06%) were paired; of these: 769s 103 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 103 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 103 pairs aligned 0 times concordantly or discordantly; of these: 769s 206 mates make up the pairs; of these: 769s 206 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 21 (16.94%) were unpaired; of these: 769s 21 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s Read 100 alignments... 769s Read 150 alignments... 769s Read 200 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing 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line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 0 alignments, 0 edits 769s --------------- 769s PASSED 769s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 769s /usr/bin/bowtie2 --cp-min 8 --local --cp-ival 4 --n-ceil 1.47818745190554,0.0409314324982333 --gbar 3 --score-min L,1.22764175354948,2.54147222453036 --rfg 27.2535869179083,10.8394183280648 -a --trim5 9 -f -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 769s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '4' because it was < 2 characters long 769s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '12' because it was < 2 characters long 769s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '19' because it was < 2 characters long 769s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '33' because it was < 2 characters long 769s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '38' because it was < 2 characters long 769s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '42' because it was < 2 characters long 769s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '43' because it was < 2 characters long 769s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '52' because it was < 2 characters long 769s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '59' because it was < 2 characters long 769s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '63' because it was < 2 characters long 769s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '76' because it was < 2 characters long 769s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '77' because it was < 2 characters long 769s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '82' because it was < 2 characters long 769s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '83' because it was < 2 characters long 769s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '87' because it was < 2 characters long 769s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '90' because it was < 2 characters long 769s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '94' because it was < 2 characters long 769s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '103' because it was < 2 characters long 769s Warning: skipping mate #2 of read '111' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '111' because it was < 2 characters long 769s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #2 of read '113' because it was < 2 characters long 769s Warning: skipping mate #1 of read '121' because length (1) <= # seed mismatches (0) 769s Warning: skipping mate #1 of read '121' because it was < 2 characters long 769s 124 reads; of these: 769s 103 (83.06%) were paired; of these: 769s 103 (100.00%) aligned concordantly 0 times 769s 0 (0.00%) aligned concordantly exactly 1 time 769s 0 (0.00%) aligned concordantly >1 times 769s ---- 769s 103 pairs aligned concordantly 0 times; of these: 769s 0 (0.00%) aligned discordantly 1 time 769s ---- 769s 103 pairs aligned 0 times concordantly or discordantly; of these: 769s 206 mates make up the pairs; of these: 769s 206 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 21 (16.94%) were unpaired; of these: 769s 21 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.1 769s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.2 769s Introducing 0 SNPs, 1/2 ref/read gaps, and 1 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 1 769s Reference gaps introduced: 1 769s Read gaps introduced: 2 769s Rearrangements introduced: 1 769s Created read sampler 769s Sampling 105 reads 769s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 769s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 769s parsing sequence Sim.pm.1... 769s parsing sequence Sim.pm.2... 769s Parsed 74 reference bases 769s *** Run 32 of 100 769s /usr/bin/bowtie2 --rfg 3.79245500422953,2.22401603499491 --rdg 36.5901937001229 --score-min L,7.86101796300455,3.28049257809383 --mm --mp 6.29496944000591,5.62331706424335 --cp-ival 2 --local --trim3 8 --trim5 0 --cp-min 3 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 769s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '11' because it was < 2 characters long 769s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '15' because it was < 2 characters long 769s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '17' because it was < 2 characters long 769s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '25' because it was < 2 characters long 769s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '28' because it was < 2 characters long 769s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '38' because it was < 2 characters long 769s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '44' because it was < 2 characters long 769s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '51' because it was < 2 characters long 769s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '52' because it was < 2 characters long 769s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '53' because it was < 2 characters long 769s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '59' because it was < 2 characters long 769s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '62' because it was < 2 characters long 769s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '63' because it was < 2 characters long 769s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '65' because it was < 2 characters long 769s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '68' because it was < 2 characters long 769s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '70' because it was < 2 characters long 769s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '71' because it was < 2 characters long 769s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '76' because it was < 2 characters long 769s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '82' because it was < 2 characters long 769s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '84' because it was < 2 characters long 769s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '100' because it was < 2 characters long 769s 105 reads; of these: 769s 105 (100.00%) were unpaired; of these: 769s 105 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s Read 50 alignments... 769s Read 100 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s /usr/bin/bowtie2 --rfg 3.79245500422953,2.22401603499491 --rdg 36.5901937001229 --score-min L,7.86101796300455,3.28049257809383 --mm --mp 6.29496944000591,5.62331706424335 --cp-ival 2 --local --trim3 8 --trim5 0 --cp-min 3 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 0 alignments, 0 edits 769s --------------- 769s PASSED 769s ALSO checking that bowtie2 and bowtie2-align match up 769s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '11' because it was < 2 characters long 769s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '15' because it was < 2 characters long 769s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '17' because it was < 2 characters long 769s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '25' because it was < 2 characters long 769s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '28' because it was < 2 characters long 769s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '38' because it was < 2 characters long 769s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '44' because it was < 2 characters long 769s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '51' because it was < 2 characters long 769s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '52' because it was < 2 characters long 769s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '53' because it was < 2 characters long 769s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '59' because it was < 2 characters long 769s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '62' because it was < 2 characters long 769s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '63' because it was < 2 characters long 769s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '65' because it was < 2 characters long 769s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '68' because it was < 2 characters long 769s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '70' because it was < 2 characters long 769s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '71' because it was < 2 characters long 769s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '76' because it was < 2 characters long 769s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '82' because it was < 2 characters long 769s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '84' because it was < 2 characters long 769s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '100' because it was < 2 characters long 769s 105 reads; of these: 769s 105 (100.00%) were unpaired; of these: 769s 105 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 769s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 769s /usr/bin/bowtie2 --rfg 3.79245500422953,2.22401603499491 --rdg 36.5901937001229 --score-min L,7.86101796300455,3.28049257809383 --mm --mp 6.29496944000591,5.62331706424335 --cp-ival 2 --local --trim3 8 --trim5 0 --cp-min 3 -f -p 4 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 769s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '11' because it was < 2 characters long 769s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '15' because it was < 2 characters long 769s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '17' because it was < 2 characters long 769s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '25' because it was < 2 characters long 769s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '28' because it was < 2 characters long 769s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '38' because it was < 2 characters long 769s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '44' because it was < 2 characters long 769s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '51' because it was < 2 characters long 769s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '52' because it was < 2 characters long 769s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '53' because it was < 2 characters long 769s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '59' because it was < 2 characters long 769s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '62' because it was < 2 characters long 769s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '63' because it was < 2 characters long 769s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '65' because it was < 2 characters long 769s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '68' because it was < 2 characters long 769s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '70' because it was < 2 characters long 769s Warning: skipping read '71' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '71' because it was < 2 characters long 769s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '76' because it was < 2 characters long 769s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '82' because it was < 2 characters long 769s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '84' because it was < 2 characters long 769s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 769s Warning: skipping read '100' because it was < 2 characters long 769s 105 reads; of these: 769s 105 (100.00%) were unpaired; of these: 769s 105 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.2 769s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.1 769s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 3 769s Reference gaps introduced: 0 769s Read gaps introduced: 0 769s Rearrangements introduced: 1 769s Created read sampler 769s Sampling 158 reads 769s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 769s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 769s parsing sequence Sim.pm.1... 769s *** Run 33 of 100 769s /usr/bin/bowtie2 -a --mm --rdg 4.14511219800196 --score-min L,4.59128356550779,7.33035531876618 --mp 2.83662200072448,1.06795072545102 --cp-ival 1 --local --cp-min 8 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 769s parsing sequence Sim.pm.2... 769s Parsed 74 reference bases 769s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '11' because it was < 2 characters long 769s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '43' because it was < 2 characters long 769s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '70' because it was < 2 characters long 769s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '96' because it was < 2 characters long 769s Warning: skipping read '115' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '115' because it was < 2 characters long 769s Warning: skipping read '136' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '136' because it was < 2 characters long 769s Warning: skipping read '140' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '140' because it was < 2 characters long 769s 158 reads; of these: 769s 158 (100.00%) were unpaired; of these: 769s 158 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s Read 50 alignments... 769s Read 100 alignments... 769s Read 150 alignments... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s /usr/bin/bowtie2 -a --mm --rdg 4.14511219800196 --score-min L,4.59128356550779,7.33035531876618 --mp 2.83662200072448,1.06795072545102 --cp-ival 1 --local --cp-min 8 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s Processing line... 769s --- Summary --- 769s Read 1 reference strings 769s Checked 0 alignments, 0 edits 769s --------------- 769s PASSED 769s ALSO checking that bowtie2 and bowtie2-align match up 769s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '11' because it was < 2 characters long 769s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '43' because it was < 2 characters long 769s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '70' because it was < 2 characters long 769s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '96' because it was < 2 characters long 769s Warning: skipping read '115' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '115' because it was < 2 characters long 769s Warning: skipping read '136' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '136' because it was < 2 characters long 769s Warning: skipping read '140' because length (1) <= # seed mismatches (0) 769s Warning: skipping read '140' because it was < 2 characters long 769s 158 reads; of these: 769s 158 (100.00%) were unpaired; of these: 769s 158 (100.00%) aligned 0 times 769s 0 (0.00%) aligned exactly 1 time 769s 0 (0.00%) aligned >1 times 769s 0.00% overall alignment rate 769s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 769s Flattened IUPAC characters 769s Mutating sequence Sim.pm.1 769s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutating sequence Sim.pm.2 769s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 769s Finished SNPs 769s Finished ref gaps 769s Finished read gaps 769s Mutated reference genome to subject genome 769s SNPs introduced: 6 769s Reference gaps introduced: 0 769s Read gaps introduced: 0 769s Rearrangements introduced: 0 769s Created read sampler 769s Sampling 175 reads 770s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 770s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 74 reference bases 770s *** Run 34 of 100 770s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --local --trim3 9 --rfg 37.3422104763276 --score-min L,8.3781011985329,5.20042142506494 --mm -a -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 770s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '16' because it was < 2 characters long 770s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '17' because it was < 2 characters long 770s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '19' because it was < 2 characters long 770s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '26' because it was < 2 characters long 770s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '27' because it was < 2 characters long 770s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '33' because it was < 2 characters long 770s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '34' because it was < 2 characters long 770s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '36' because it was < 2 characters long 770s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '37' because it was < 2 characters long 770s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '39' because it was < 2 characters long 770s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '40' because it was < 2 characters long 770s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '42' because it was < 2 characters long 770s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '43' because it was < 2 characters long 770s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '44' because it was < 2 characters long 770s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '46' because it was < 2 characters long 770s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '54' because it was < 2 characters long 770s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '55' because it was < 2 characters long 770s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '62' because it was < 2 characters long 770s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '66' because it was < 2 characters long 770s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '68' because it was < 2 characters long 770s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '76' because it was < 2 characters long 770s Warning: skipping mate #2 of read '76' because it was < 2 characters long 770s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '77' because it was < 2 characters long 770s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '79' because it was < 2 characters long 770s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 770s Read 50 alignments... 770s Read 100 alignments... 770s Warning: skipping mate #1 of read '82' because it was < 2 characters long 770s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '86' because it was < 2 characters long 770s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '90' because it was < 2 characters long 770s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '97' because it was < 2 characters long 770s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '98' because it was < 2 characters long 770s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '101' because it was < 2 characters long 770s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '102' because it was < 2 characters long 770s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '108' because it was < 2 characters long 770s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '113' because it was < 2 characters long 770s Warning: skipping mate #2 of read '113' because it was < 2 characters long 770s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '114' because it was < 2 characters long 770s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '115' because it was < 2 characters long 770s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '119' because it was < 2 characters long 770s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '130' because it was < 2 characters long 770s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '132' because it was < 2 characters long 770s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '145' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '145' because it was < 2 characters long 770s Warning: skipping mate #2 of read '145' because it was < 2 characters long 770s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '148' because it was < 2 characters long 770s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '151' because it was < 2 characters long 770s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '153' because it was < 2 characters long 770s Warning: skipping mate #1 of read '154' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '154' because it was < 2 characters long 770s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '156' because it was < 2 characters long 770s Read 150 alignments... 770s Read 200 alignments... 770s Warning: skipping mate #1 of read '165' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '165' because it was < 2 characters long 770s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '167' because it was < 2 characters long 770s Warning: skipping mate #1 of read '173' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '173' because it was < 2 characters long 770s 175 reads; of these: 770s 148 (84.57%) were paired; of these: 770s 148 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 148 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 148 pairs aligned 0 times concordantly or discordantly; of these: 770s 296 mates make up the pairs; of these: 770s 296 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 27 (15.43%) were unpaired; of these: 770s 27 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 0.00% overall alignment rate 770s Read 250 alignments... 770s Read 300 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --local --trim3 9 --rfg 37.3422104763276 --score-min L,8.3781011985329,5.20042142506494 --mm -a -q -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s 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Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 0 alignments, 0 edits 770s --------------- 770s PASSED 770s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 770s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '16' because it was < 2 characters long 770s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '17' because it was < 2 characters long 770s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '19' because it was < 2 characters long 770s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '26' because it was < 2 characters long 770s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '27' because it was < 2 characters long 770s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '33' because it was < 2 characters long 770s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '34' because it was < 2 characters long 770s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '36' because it was < 2 characters long 770s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '37' because it was < 2 characters long 770s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '39' because it was < 2 characters long 770s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '40' because it was < 2 characters long 770s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '42' because it was < 2 characters long 770s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '43' because it was < 2 characters long 770s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '44' because it was < 2 characters long 770s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '46' because it was < 2 characters long 770s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '54' because it was < 2 characters long 770s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '55' because it was < 2 characters long 770s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '62' because it was < 2 characters long 770s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '66' because it was < 2 characters long 770s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '68' because it was < 2 characters long 770s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '76' because it was < 2 characters long 770s Warning: skipping mate #2 of read '76' because it was < 2 characters long 770s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '77' because it was < 2 characters long 770s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '79' because it was < 2 characters long 770s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '82' because it was < 2 characters long 770s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '86' because it was < 2 characters long 770s Warning: skipping mate #1 of read '90' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '90' because it was < 2 characters long 770s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '97' because it was < 2 characters long 770s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '98' because it was < 2 characters long 770s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '101' because it was < 2 characters long 770s Warning: skipping mate #1 of read '102' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '102' because it was < 2 characters long 770s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '108' because it was < 2 characters long 770s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '113' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '113' because it was < 2 characters long 770s Warning: skipping mate #2 of read '113' because it was < 2 characters long 770s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '114' because it was < 2 characters long 770s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '115' because it was < 2 characters long 770s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '119' because it was < 2 characters long 770s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '130' because it was < 2 characters long 770s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '132' because it was < 2 characters long 770s Warning: skipping mate #1 of read '145' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '145' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '145' because it was < 2 characters long 770s Warning: skipping mate #2 of read '145' because it was < 2 characters long 770s Warning: skipping read '148' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '148' because it was < 2 characters long 770s Warning: skipping mate #1 of read '151' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '151' because it was < 2 characters long 770s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '153' because it was < 2 characters long 770s Warning: skipping mate #1 of read '154' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '154' because it was < 2 characters long 770s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '156' because it was < 2 characters long 770s Warning: skipping mate #1 of read '165' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '165' because it was < 2 characters long 770s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '167' because it was < 2 characters long 770s Warning: skipping mate #1 of read '173' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '173' because it was < 2 characters long 770s 175 reads; of these: 770s 148 (84.57%) were paired; of these: 770s 148 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 148 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 148 pairs aligned 0 times concordantly or discordantly; of these: 770s 296 mates make up the pairs; of these: 770s 296 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 27 (15.43%) were unpaired; of these: 770s 27 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 0.00% overall alignment rate 770s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 770s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 770s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.1 770s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.2 770s Introducing 8 SNPs, 0/2 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 10 770s Reference gaps introduced: 0 770s Read gaps introduced: 3 770s Rearrangements introduced: 0 770s Created read sampler 770s Sampling 78 reads 770s *** Run 35 of 100 770s /usr/bin/bowtie2 --mm --score-min L,6.48015601831175,2.87558276039759 --rdg 30.7465858750324,9.23427254097218 --nofw --mp 4.45010509447145,3.68126898161502 --cp-ival 2 --np 1 --cp-min 11 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 770s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 770s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 74 reference bases 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 770s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '23' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 770s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '24' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 770s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '29' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 770s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '69' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 770s Read 50 alignments... 770s Read 100 alignments... 770s 78 reads; of these: 770s 78 (100.00%) were paired; of these: 770s 77 (98.72%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 1 (1.28%) aligned concordantly >1 times 770s ---- 770s 77 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 77 pairs aligned 0 times concordantly or discordantly; of these: 770s 154 mates make up the pairs; of these: 770s 145 (94.16%) aligned 0 times 770s 8 (5.19%) aligned exactly 1 time 770s 1 (0.65%) aligned >1 times 770s 7.05% overall alignment rate 770s Read 150 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s ACCTC 770s ACCTC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AAC 770s AAC 770s Processing line... 770s CTC 770s CTC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GTG 770s GTG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GACG 770s GACG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GA 770s GA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s ATAAC 770s ATAAC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CAGTT 770s CAGTT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AAAC 770s AAAC 770s Processing line... 770s Processing line... 770s ACGCAGTTACC 770s ACGCAGTTACC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GTC 770s GTC 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 11 alignments, 0 edits 770s --------------- 770s PASSED 770s ALSO checking that bowtie2 and bowtie2-align match up 770s /usr/bin/bowtie2 --mm --score-min L,6.48015601831175,2.87558276039759 --rdg 30.7465858750324,9.23427254097218 --nofw --mp 4.45010509447145,3.68126898161502 --cp-ival 2 --np 1 --cp-min 11 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 770s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '23' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 770s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '24' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 770s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '29' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 770s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 770s /usr/bin/bowtie2 --mm --score-min L,6.48015601831175,2.87558276039759 --rdg 30.7465858750324,9.23427254097218 --nofw --mp 4.45010509447145,3.68126898161502 --cp-ival 2 --np 1 --cp-min 11 -q -p 4 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 770s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '69' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 770s 78 reads; of these: 770s 78 (100.00%) were paired; of these: 770s 77 (98.72%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 1 (1.28%) aligned concordantly >1 times 770s ---- 770s 77 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 77 pairs aligned 0 times concordantly or discordantly; of these: 770s 154 mates make up the pairs; of these: 770s 145 (94.16%) aligned 0 times 770s 8 (5.19%) aligned exactly 1 time 770s 1 (0.65%) aligned >1 times 770s 7.05% overall alignment rate 770s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 770s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '23' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 770s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '24' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 770s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '29' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 770s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '69' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 770s 78 reads; of these: 770s 78 (100.00%) were paired; of these: 770s 77 (98.72%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 1 (1.28%) aligned concordantly >1 times 770s ---- 770s 77 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 77 pairs aligned 0 times concordantly or discordantly; of these: 770s 154 mates make up the pairs; of these: 770s 145 (94.16%) aligned 0 times 770s 8 (5.19%) aligned exactly 1 time 770s 1 (0.65%) aligned >1 times 770s 7.05% overall alignment rate 770s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 770s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.2 770s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 770s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.1 770s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 9 770s Reference gaps introduced: 1 770s Read gaps introduced: 1 770s Rearrangements introduced: 0 770s Created read sampler 770s Sampling 49 reads 770s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 770s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 74 reference bases 770s *** Run 36 of 100 770s /usr/bin/bowtie2 --cp-min 7 -i C,4.63590974642538,1.63985801552792 --trim5 5 --local --cp-ival 2 --mp 3.55817457635181,1.56427714925425 --trim3 4 --rdg 21.1200797540167,16.5033979373001 --score-min L,2.9117665744853,1.203380434442 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 770s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '2' because it was < 2 characters long 770s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '6' because it was < 2 characters long 770s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '7' because it was < 2 characters long 770s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '8' because it was < 2 characters long 770s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '10' because it was < 2 characters long 770s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '15' because it was < 2 characters long 770s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '17' because it was < 2 characters long 770s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '18' because it was < 2 characters long 770s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '19' because it was < 2 characters long 770s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '21' because it was < 2 characters long 770s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '24' because it was < 2 characters long 770s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '32' because it was < 2 characters long 770s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '34' because it was < 2 characters long 770s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '38' because it was < 2 characters long 770s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '40' because it was < 2 characters long 770s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '41' because it was < 2 characters long 770s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '42' because it was < 2 characters long 770s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '45' because it was < 2 characters long 770s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '46' because it was < 2 characters long 770s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '47' because it was < 2 characters long 770s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '49' because it was < 2 characters long 770s 49 reads; of these: 770s 49 (100.00%) were unpaired; of these: 770s 43 (87.76%) aligned 0 times 770s 4 (8.16%) aligned exactly 1 time 770s 2 (4.08%) aligned >1 times 770s 12.24% overall alignment rate 770s Read 50 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CAACGCAGTAACCTCCTGAAAACA 770s CAACGCAGTTACCTCCTGAAAACA 770s Processing line... 770s Processing line... 770s ATAGACGACGTAACAACGCAGTTACCT 770s ATAGACGACNTAACAACGCAGTTACCT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s ACA 770s ACA 770s Processing line... 770s Processing line... 770s Processing line... 770s CGC 770s CGC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CGA 770s CGA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s ACCGAGATATGAGTG 770s ACCGAGATATGAGTG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 6 alignments, 0 edits 770s --------------- 770s PASSED 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.1 770s Introducing 1 SNPs, 0/2 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.2 770s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 5 770s Reference gaps introduced: 0 770s Read gaps introduced: 2 770s Rearrangements introduced: 0 770s Created read sampler 770s Sampling 169 reads 770s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 770s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 74 reference bases 770s *** Run 37 of 100 770s /usr/bin/bowtie2 --ma 18.4551300013839 --cp-min 6 --cp-ival 3 --n-ceil 0.243959055857975,0.403608261750407 --score-min L,3.71259266630298,5.86739564674377 --rfg 6.31602344515826 --rdg 15.8711550380328,17.6393317134786 -M 6 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 770s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 770s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 770s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '2' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 770s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '3' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 770s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '6' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 770s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '27' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 770s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '39' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 770s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '51' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 770s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '70' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 770s Warning: skipping mate #1 of read '93' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '93' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 770s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '113' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 770s Read 50 alignments... 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 770s Warning: skipping mate #1 of read '131' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '131' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 770s Read 100 alignments... 770s Read 150 alignments... 770s 169 reads; of these: 770s 169 (100.00%) were paired; of these: 770s 169 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 169 pairs aligned concordantly 0 times; of these: 770s 1 (0.59%) aligned discordantly 1 time 770s ---- 770s 168 pairs aligned 0 times concordantly or discordantly; of these: 770s 336 mates make up the pairs; of these: 770s 278 (82.74%) aligned 0 times 770s 43 (12.80%) aligned exactly 1 time 770s 15 (4.46%) aligned >1 times 770s 17.75% overall alignment rate 770s Read 200 alignments... 770s Read 250 alignments... 770s Read 300 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AAC 770s AAC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CAGTTACCTCCTGAAA 770s CAGTTACCTCCTGAAA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AACAACGCAGTTACCT 770s AACAACGCAGTTACCT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AGACGA 770s AGACGA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAACGTC 770s TAACGTC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s ACGCAGTTACCTC 770s ACGCAGTTACCTC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AATAA 770s AATAA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CAG 770s CAG 770s Processing line... 770s Processing line... 770s AACAACGCAGTTACCTCCTGAA 770s AACAACGCAGTTACCTCCTGAA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAACG 770s TAACG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CTCCTGA 770s CTCCTGA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CAGTTA 770s CAGTTA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GATA 770s GATA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CAG 770s CAG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AACAACGCAGTTA 770s AACAACGCAGTTA 770s Processing line... 770s Processing line... 770s CTGAAA 770s CTGAAA 770s Processing line... 770s Processing line... 770s CAACGCAGTTACCTCCTGA 770s CAACGCAGTTACCTCCTGA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAACAACGCAGTTA 770s TAACAACGCAGTTA 770s Processing line... 770s Processing line... 770s ATA 770s ATA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TTAC 770s TTAC 770s Processing line... 770s Processing line... 770s CAACGCAGTTACCTCCTGAAAA 770s CAACGCAGTTACCTCCTGAAAA 770s Processing line... 770s Processing line... 770s CGAGATATGAGTGATTAATAACG 770s CGAGATATGAGTGATTAATAACG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CT 770s CT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TTACCTCC 770s TTACCTCC 770s Processing line... 770s Processing line... 770s AGTTACC 770s AGTTACC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AACGCAGTTACCTCCT 770s AACGCAGTTACCTCCT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s ACCG 770s ACCG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CGCAGTTACCTCCTG 770s CGCAGTTACCTCCTG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AACG 770s AACG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GTTACCTCCTGAAAA 770s GTTACCTCCTGAAAA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAACAACGCAGTTACCTCCT 770s TAACAACGCAGTTACCTCCT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AGTTACCTCC 770s AGTTACCTCC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GC 770s GC 770s Processing line... 770s Processing line... 770s AACAACGCAGTTACCT 770s AACAACGCAGTTACCT 770s Processing line... 770s Processing line... 770s TGAAAACA 770s TGAAAACA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAT 770s TAT 770s Processing line... 770s Processing line... 770s CTCCTGAAAACA 770s CTCCTGAAAACA 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AACGCAGTTAC 770s AACGCAGTTAC 770s Processing line... 770s Processing line... 770s CCTGA 770s CCTGA 770s Processing line... 770s CTGAAAACAT 770s CTGAAAACAT 770s Processing line... 770s AACAACGCAGTTACCTCCTGAA 770s AACAACGCAGTTACCTCCTGAA 770s Processing line... 770s Processing line... 770s CAGTTACCTCCTG 770s CAGTTACCTCCTG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CGC 770s CGC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TAACAACGCAGTTAC 770s TAACAACGCAGTTAC 770s Processing line... 770s ACG 770s ACG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s CGT 770s CGT 770s Processing line... 770s CTCC 770s CTCC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TTACCT 770s TTACCT 770s Processing line... 770s Processing line... 770s AC 770s AC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AACA 770s AACA 770s Processing line... 770s Processing line... 770s TACCTCCTG 770s TACCTCCTG 770s Processing line... 770s Processing line... 770s TGAGTGATTAATAACG 770s TGAGTGATTAATAACG 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TT 770s TT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s TACCTCC 770s TACCTCC 770s Processing line... 770s Processing line... 770s ACGCAGTTA 770s ACGCAGTTA 770s Processing line... 770s GAT 770s GAT 770s Processing line... 770s CAACGCAGTTACCT 770s CAACGCAGTTACCT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AACAACGCAGTTACCTCCTGAAAACATC 770s AACAACGCAGTTACCTCCTGAAAACATC 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s AGT 770s AGT 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s GTTACCTCCTGAAAACATCC 770s GTTACCTCCTGAAAACATCC 770s Processing line... 770s Processing line... 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 60 alignments, 0 edits 770s --------------- 770s PASSED 770s ALSO checking that bowtie2 and bowtie2-align match up 770s /usr/bin/bowtie2 --ma 18.4551300013839 --cp-min 6 --cp-ival 3 --n-ceil 0.243959055857975,0.403608261750407 --score-min L,3.71259266630298,5.86739564674377 --rfg 6.31602344515826 --rdg 15.8711550380328,17.6393317134786 -M 6 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 770s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 770s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 770s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '2' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 770s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '3' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 770s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '6' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 770s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '27' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 770s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '39' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 770s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '51' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 770s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '70' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 770s Warning: skipping mate #1 of read '93' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '93' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 770s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '113' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 770s Warning: skipping mate #1 of read '131' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '131' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 770s 169 reads; of these: 770s 169 (100.00%) were paired; of these: 770s 169 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 169 pairs aligned concordantly 0 times; of these: 770s 1 (0.59%) aligned discordantly 1 time 770s ---- 770s 168 pairs aligned 0 times concordantly or discordantly; of these: 770s 336 mates make up the pairs; of these: 770s 278 (82.74%) aligned 0 times 770s 43 (12.80%) aligned exactly 1 time 770s 15 (4.46%) aligned >1 times 770s 17.75% overall alignment rate 770s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 770s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 770s /usr/bin/bowtie2 --ma 18.4551300013839 --cp-min 6 --cp-ival 3 --n-ceil 0.243959055857975,0.403608261750407 --score-min L,3.71259266630298,5.86739564674377 --rfg 6.31602344515826 --rdg 15.8711550380328,17.6393317134786 -M 6 -f -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 770s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 770s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 770s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '2' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 770s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '3' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 770s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '6' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 770s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '27' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 770s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '39' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 770s Warning: skipping mate #2 of read '51' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #2 of read '51' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 770s Warning: skipping mate #1 of read '70' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '70' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 770s Warning: skipping mate #1 of read '93' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '93' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 770s Warning: skipping mate #1 of read '113' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '113' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 770s Warning: skipping mate #1 of read '131' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read '131' because it was < 2 characters long 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 770s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 770s 169 reads; of these: 770s 169 (100.00%) were paired; of these: 770s 169 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 169 pairs aligned concordantly 0 times; of these: 770s 1 (0.59%) aligned discordantly 1 time 770s ---- 770s 168 pairs aligned 0 times concordantly or discordantly; of these: 770s 336 mates make up the pairs; of these: 770s 278 (82.74%) aligned 0 times 770s 43 (12.80%) aligned exactly 1 time 770s 15 (4.46%) aligned >1 times 770s 17.75% overall alignment rate 770s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 770s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 770s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.2 770s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.1 770s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 3 770s Reference gaps introduced: 1 770s Read gaps introduced: 0 770s Rearrangements introduced: 0 770s Created read sampler 770s Sampling 89 reads 770s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 770s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 74 reference bases 770s *** Run 38 of 100 770s /usr/bin/bowtie2 --gbar 7 --rfg 39.352052733267 --score-min L,9.35129865485262,5.40868246170599 --trim3 6 --cp-ival 2 --local --mp 4.31548552579073,4.1318839277188 --trim5 5 -M 5 --np 6 --cp-min 3 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 770s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 770s /usr/bin/bowtie2 --gbar 7 --rfg 39.352052733267 --score-min L,9.35129865485262,5.40868246170599 --trim3 6 --cp-ival 2 --local --mp 4.31548552579073,4.1318839277188 --trim5 5 -M 5 --np 6 --cp-min 3 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 770s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 770s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 770s Read 50 alignments... 770s Read 100 alignments... 770s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 770s 89 reads; of these: 770s 76 (85.39%) were paired; of these: 770s 76 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 76 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 76 pairs aligned 0 times concordantly or discordantly; of these: 770s 152 mates make up the pairs; of these: 770s 152 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 13 (14.61%) were unpaired; of these: 770s 13 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 0.00% overall alignment rate 770s Read 150 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s P*** Run 39 of 100 770s /usr/bin/bowtie2 --mp 9.85914154165752,6.10964479917652 -N 0 -L22 --cp-ival 3 --n-ceil 0.440387006584972,0.571259064626424 --local -a --rdg 13.1842104022661,16.0031296202289 --rfg 23.8938149493068,18.8358174269295 --score-min L,4.94064154240979,4.29460902467452 -R 4 --cp-min 2 --trim5 3 --np 2 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 770s rocessing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 0 alignments, 0 edits 770s --------------- 770s PASSED 770s ALSO checking that bowtie2 and bowtie2-align match up 770s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 770s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 770s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 770s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 770s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 770s 89 reads; of these: 770s 76 (85.39%) were paired; of these: 770s 76 (100.00%) aligned concordantly 0 times 770s 0 (0.00%) aligned concordantly exactly 1 time 770s 0 (0.00%) aligned concordantly >1 times 770s ---- 770s 76 pairs aligned concordantly 0 times; of these: 770s 0 (0.00%) aligned discordantly 1 time 770s ---- 770s 76 pairs aligned 0 times concordantly or discordantly; of these: 770s 152 mates make up the pairs; of these: 770s 152 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 13 (14.61%) were unpaired; of these: 770s 13 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 0.00% overall alignment rate 770s Flattened IUPAC characters 770s Mutating sequence Sim.pm.2 770s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutating sequence Sim.pm.1 770s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 770s Finished SNPs 770s Finished ref gaps 770s Finished read gaps 770s Mutated reference genome to subject genome 770s SNPs introduced: 7 770s Reference gaps introduced: 0 770s Read gaps introduced: 0 770s Rearrangements introduced: 0 770s Created read sampler 770s Sampling 48 reads 770s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 770s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 770s parsing sequence Sim.pm.1... 770s parsing sequence Sim.pm.2... 770s Parsed 74 reference bases 770s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '12' because it was < 2 characters long 770s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '13' because it was < 2 characters long 770s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '16' because it was < 2 characters long 770s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '19' because it was < 2 characters long 770s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '22' because it was < 2 characters long 770s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '24' because it was < 2 characters long 770s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '29' because it was < 2 characters long 770s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '31' because it was < 2 characters long 770s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '40' because it was < 2 characters long 770s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '46' because it was < 2 characters long 770s 48 reads; of these: 770s 48 (100.00%) were unpaired; of these: 770s 48 (100.00%) aligned 0 times 770s 0 (0.00%) aligned exactly 1 time 770s 0 (0.00%) aligned >1 times 770s 0.00% overall alignment rate 770s Read 50 alignments... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s Processing line... 770s --- Summary --- 770s Read 1 reference strings 770s Checked 0 alignments, 0 edits 770s --------------- 770s PASSED 770s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 770s /usr/bin/bowtie2 --mp 9.85914154165752,6.10964479917652 -N 0 -L22 --cp-ival 3 --n-ceil 0.440387006584972,0.571259064626424 --local -a --rdg 13.1842104022661,16.0031296202289 --rfg 23.8938149493068,18.8358174269295 --score-min L,4.94064154240979,4.29460902467452 -R 4 --cp-min 2 --trim5 3 --np 2 -q -p 4 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 770s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '12' because it was < 2 characters long 770s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '13' because it was < 2 characters long 770s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '16' because it was < 2 characters long 770s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '19' because it was < 2 characters long 770s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '22' because it was < 2 characters long 770s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '24' because it was < 2 characters long 770s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '29' because it was < 2 characters long 770s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '31' because it was < 2 characters long 770s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 770s Warning: skipping read '40' because it was < 2 characters long 770s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 770s Warning: skipping read '46' because it was < 2 characters long 771s 48 reads; of these: 771s 48 (100.00%) were unpaired; of these: 771s 48 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 0.00% overall alignment rate 771s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 771s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 771s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.1 771s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.2 771s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 3 771s Reference gaps introduced: 0 771s Read gaps introduced: 1 771s Rearrangements introduced: 3 771s Created read sampler 771s Sampling 146 reads 771s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 771s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s *** Run 40 of 100 771s /usr/bin/bowtie2 --mm --score-min L,1.25430521723625,2.26823714459322 --trim3 1 --cp-ival 1 --cp-min 3 --nofw --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 771s Parsed 74 reference bases 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 771s Read 50 alignments... 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 771s Read 100 alignments... 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 771s Read 150 alignments... 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 771s 146 reads; of these: 771s 145 (99.32%) were paired; of these: 771s 144 (99.31%) aligned concordantly 0 times 771s 1 (0.69%) aligned concordantly exactly 1 time 771s 0 (0.00%) aligned concordantly >1 times 771s ---- 771s 144 pairs aligned concordantly 0 times; of these: 771s 0 (0.00%) aligned discordantly 1 time 771s ---- 771s 144 pairs aligned 0 times concordantly or discordantly; of these: 771s 288 mates make up the pairs; of these: 771s 251 (87.15%) aligned 0 times 771s 28 (9.72%) aligned exactly 1 time 771s 9 (3.12%) aligned >1 times 771s 1 (0.68%) were unpaired; of these: 771s 1 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 13.40% overall alignment rate 771s Read 200 alignments... 771s Read 250 alignments... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TTACCTCCTGAAAAC 771s TTACCTCCTGAAAAC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TAACAACGCAGTTACCTCCTGA 771s TAACAACGCAGTTACCTCCTGA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACAA 771s ACAA 771s Processing line... 771s /usr/bin/bowtie2 --mm --score-min L,1.25430521723625,2.26823714459322 --trim3 1 --cp-ival 1 --cp-min 3 --nofw --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 771s Processing line... 771s Processing line... 771s Processing line... 771s TC 771s TC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CCTG 771s CCTG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CCTCC 771s CCTCC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GTT 771s GTT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GA 771s GA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACATC 771s ACATC 771s Processing line... 771s Processing line... 771s TAACAACGCAGTTACCTCC 771s TAACAACGCAGTTACCTCC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TGAAAAC 771s TGAAAAC 771s Processing line... 771s ACGCAGTTACCTCCTGAA 771s ACGCAGTTACCTCCTGAA 771s Processing line... 771s Processing line... 771s Processing line... 771s TGAAAACATC 771s TGAAAACATC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TA 771s TA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GAAAACA 771s GAAAACA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CT 771s CT 771s Processing line... 771s Processing line... 771s AAA 771s AAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CTGAA 771s CTGAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GACG 771s GACG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACCTCCTGAAAAC 771s ACCTCCTGAAAAC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AATAA 771s AATAA 771s Processing line... 771s Processing line... 771s CTCCTGAA 771s CTCCTGAA 771s Processing line... 771s Processing line... 771s AGTTA 771s AGTTA 771s Processing line... 771s Processing line... 771s TAACAACGCAGTTACCTCCTGAAA 771s TAACAACGCAGTTACCTCCTGAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AACGCAGTTACCTCCTGAAA 771s AACGCAGTTACCTCCTGAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TAACAACGCAGTTACCTC 771s TAACAACGCAGTTACCTC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GT 771s GT 771s Processing line... 771s Processing line... 771s AA 771s AA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TAC 771s TAC 771s Processing line... 771s Processing line... 771s AAT 771s AAT 771s Processing line... 771s Processing line... 771s TCT 771s TCT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GCAGTTACCTC 771s GCAGTTACCTC 771s Processing line... 771s Processing line... 771s CAACGCAG 771s CAACGCAG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ATC 771s ATC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TC 771s TC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACCTC 771s ACCTC 771s Processing line... 771s Processing line... 771s AG 771s AG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TTACCTCCTGAAA 771s TTACCTCCTGAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CCTGAAA 771s CCTGAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s --- Summary --- 771s Read 1 reference strings 771s Checked 39 alignments, 0 edits 771s --------------- 771s PASSED 771s ALSO checking that bowtie2 and bowtie2-align match up 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 771s 146 reads; of these: 771s 145 (99.32%) were paired; of these: 771s 144 (99.31%) aligned concordantly 0 times 771s 1 (0.69%) aligned concordantly exactly 1 time 771s 0 (0.00%) aligned concordantly >1 times 771s ---- 771s 144 pairs aligned concordantly 0 times; of these: 771s 0 (0.00%) aligned discordantly 1 time 771s ---- 771s 144 pairs aligned 0 times concordantly or discordantly; of these: 771s 288 mates make up the pairs; of these: 771s 251 (87.15%) aligned 0 times 771s 28 (9.72%) aligned exactly 1 time 771s 9 (3.12%) aligned >1 times 771s 1 (0.68%) were unpaired; of these: 771s 1 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 13.40% overall alignment rate 771s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 771s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 771s /usr/bin/bowtie2 --mm --score-min L,1.25430521723625,2.26823714459322 --trim3 1 --cp-ival 1 --cp-min 3 --nofw --qseq -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 771s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 771s 146 reads; of these: 771s 145 (99.32%) were paired; of these: 771s 144 (99.31%) aligned concordantly 0 times 771s 1 (0.69%) aligned concordantly exactly 1 time 771s 0 (0.00%) aligned concordantly >1 times 771s ---- 771s 144 pairs aligned concordantly 0 times; of these: 771s 0 (0.00%) aligned discordantly 1 time 771s ---- 771s 144 pairs aligned 0 times concordantly or discordantly; of these: 771s 288 mates make up the pairs; of these: 771s 251 (87.15%sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 771s ) aligned 0 times 771s 28 (9.72%) aligned exactly 1 time 771s 9 (3.12%) aligned >1 times 771s 1 (0.68%) were unpaired; of these: 771s 1 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 13.40% overall alignment rate 771s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 771s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 771s *** Run 41 of 100 771s /usr/bin/bowtie2 --cp-min 2 -D 28 --cp-ival 1 --trim3 3 -R 3 --np 1 --gbar 5 --score-min L,1.02807307354464,4.73656774433714 --rfg 21.8885532177645,9.35904259864177 -a -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.1 771s Introducing 1 SNPs, 2/0 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.2 771s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 2 771s Reference gaps introduced: 2 771s Read gaps introduced: 1 771s Rearrangements introduced: 0 771s Created read sampler 771s Sampling 35 reads 771s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 771s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 74 reference bases 771s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 771s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '6' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 771s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '28' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 771s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '29' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 771s 35 reads; of these: 771s 35 (100.00%) were unpaired; of these: 771s 28 (80.00%) aligned 0 times 771s 6 (17.14%) aligned exactly 1 time 771s 1 (2.86%) aligned >1 times 771s 20.00% overall alignment rate 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s /usr/bin/bowtie2 --cp-min 2 -D 28 --cp-ival 1 --trim3 3 -R 3 --np 1 --gbar 5 --score-min L,1.02807307354464,4.73656774433714 --rfg 21.8885532177645,9.35904259864177 -a -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 771s GTGATTAATAACGTCT 771s GTGATTAATAACGTCT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACAACGCAGT 771s ACAACGCAGT 771s Processing line... 771s CAA 771s CAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GTTACCTCC 771s GTTACCTCC 771s Processing line... 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s TT 771s TT 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s TT 771s TT 771s Processing line... 771s AA 771s AA 771s Processing line... 771s Processing line... 771s Processing line... 771s TACCT 771s TACCT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TACCT 771s TACCT 771s --- Summary --- 771s Read 1 reference strings 771s Checked 16 alignments, 0 edits 771s --------------- 771s PASSED 771s ALSO checking that bowtie2 and bowtie2-align match up 771s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 771s Warning: skipping read '6' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '6' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 771s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '28' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 771s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '29' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 771s 35 reads; of these: 771s 35 (100.00%) were unpaired; of these: 771s 28 (80.00%) aligned 0 times 771s 6 (17.14%) aligned exactly 1 time 771s 1 (2.86%) aligned >1 times 771s 20.00% overall alignment rate 771s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.1 771s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.2 771s Introducing 4 SNPs, 3/2 ref/read gaps, and 0 rearrangements 771s *** Run 42 of 100 771s /usr/bin/bowtie2 -M 3 --norc --cp-min 4 --mm --score-min L,1.24150127290171,4.31329908111618 --rfg 9.98865887244978 --cp-ival 2 --local --n-ceil 1.20792355280067,1.20899440453599 --mp 8.55128706193501,5.69192339284974 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 4 771s Reference gaps introduced: 3 771s Read gaps introduced: 2 771s Rearrangements introduced: 0 771s Created read sampler 771s Sampling 132 reads 771s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 771s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 74 reference bases 771s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 771s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '8' because it was < 2 characters long 771s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '15' because it was < 2 characters long 771s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '24' because it was < 2 characters long 771s Warning: skipping read '61' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '61' because it was < 2 characters long 771s Warning: skipping read '98' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '98' because it was < 2 characters long 771s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '110' because it was < 2 characters long 771s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '111' because it was < 2 characters long 771s 132 reads; of these: 771s 132 (100.00%) were unpaired; of these: 771s 132 (100.00%) aligned 0 times 771s 0 (0.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 0.00% overall alignment rate 771s Read 50 alignments... 771s Read 100 alignments... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s --- Summary --- 771s Read 1 reference strings 771s Checked 0 alignments, 0 edits 771s --------------- 771s PASSED 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.1 771s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.2 771s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 9 771s Reference gaps introduced: 0 771s Read gaps introduced: 1 771s Rearrangements introduced: 1 771s Created read sampler 771s Sampling 140 reads 771s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 771s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 74 reference bases 771s *** Run 43 of 100 771s /usr/bin/bowtie2 -R 3 --cp-min 3 --trim5 6 --norc --n-ceil 0.253234293556267,0.873871310976828 --cp-ival 1 --mm --rfg 3.01689883574676 --rdg 20.8929045460638,19.2446751728642 --score-min L,1.23473201410483,2.15645158258192 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 771s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 771s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 771s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '4' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 771s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '5' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 771s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '6' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 771s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '7' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 771s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '8' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 771s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '10' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 771s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '12' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 771s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '19' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 771s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '28' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 771s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '33' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 771s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '37' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 771s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '43' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 771s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '47' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 771s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '49' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 771s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '51' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 771s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '53' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 771s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '63' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 771s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '66' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 771s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '70' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 771s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '74' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 771s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '75' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 771s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '78' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 771s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '79' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 771s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '81' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 771s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '82' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 771s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '83' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 771s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '85' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 771s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '88' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 771s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '93' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 771s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '107' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 771s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '116' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 771s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '119' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 771s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '121' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 771s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '126' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 771s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '129' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 771s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '130' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 771s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '134' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 771s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '139' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 771s 140 reads; of these: 771s 140 (100.00%) were unpaired; of these: 771s 123 (87.86%) aligned 0 times 771s 13 (9.29%) aligned exactly 1 time 771s 4 (2.86%) aligned >1 times 771s 12.14% overall alignment rate 771s Read 50 alignments... 771s Read 100 alignments... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s /usr/bin/bowtie2 -R 3 --cp-min 3 --trim5 6 --norc --n-ceil 0.253234293556267,0.873871310976828 --cp-ival 1 --mm --rfg 3.01689883574676 --rdg 20.8929045460638,19.2446751728642 --score-min L,1.23473201410483,2.15645158258192 -f -p 4 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 771s Processing line... 771s ATAG 771s ATAG 771s Processing line... 771s Processing line... 771s GATAT 771s GATAT 771s Processing line... 771s Processing line... 771s Processing line... 771s CGAGATATGAGTGATTA 771s CGAGATATGAGTGATTA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CT 771s CT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GAGTGA 771s GAGTGA 771s Processing line... 771s AACGCAGTTACCTCCTGAAAACATCC 771s AACGCAGTTACCTCCTGAAAACATCC 771s Processing line... 771s CTCCTG 771s CTCCTG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CTGAAAA 771s CTGAAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TTACCTCCTGA 771s TTACCTCCTGA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ATCC 771s ATCC 771s Processing line... 771s Processing line... 771s GTG 771s GTG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CTCCTG 771s CTCCTG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AAAA 771s AAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AG 771s AG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GAC 771s GAC 771s Processing line... 771s Processing line... 771s Processing line... 771s TA 771s TA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CCG 771s CCG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s --- Summary --- 771s Read 1 reference strings 771s Checked 17 alignments, 0 edits 771s --------------- 771s PASSED 771s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 771s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 771s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 771s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '4' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 771s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '5' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 771s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '6' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 771s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '7' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 771s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '8' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 771s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '10' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 771s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '12' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 771s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '19' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 771s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '28' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 771s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '33' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 771s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '37' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 771s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '43' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 771s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '47' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 771s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '49' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 771s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '51' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 771s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '53' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 771s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '63' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 771s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '66' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 771s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '70' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 771s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '74' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 771s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '75' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 771s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '78' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 771s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '79' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 771s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '81' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 771s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '82' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 771s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '83' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 771s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '85' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 771s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '88' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 771s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '93' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 771s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '107' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 771s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '116' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 771s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '119' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 771s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '121' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 771s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '126' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 771s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '129' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 771s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '130' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 771s Warning: skipping read '134' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '134' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 771s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '139' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 771s 140 reads; of these: 771s 140 (100.00%) were unpaired; of these: 771s 123 (87.86%) aligned 0 times 771s 13 (9.29%) aligned exactly 1 time 771s 4 (2.86%) aligned >1 times 771s 12.14% overall alignment rate 771s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.2 771s Introducing 7 SNPs, 0/2 ref/read gaps, and 1 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.1 771s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 8 771s Reference gaps introduced: 0 771s Read gaps introduced: 2 771s Rearrangements introduced: 1 771s Created read sampler 771s Sampling 174 reads 771s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 771s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 74 reference bases 771s *** Run 44 of 100 771s /usr/bin/bowtie2 -R 3 --cp-min 8 -i S,0.82744940339271,5.04024650828026 --trim5 5 -M 2 --np 3 --trim3 8 -N 0 -L19 --cp-ival 1 --rdg 44.2981916164729 --rfg 46.4732593960255,5.37773597897383 --score-min L,9.40683052576175,5.31927337177947 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 771s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 771s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '7' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 771s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '12' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 771s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '16' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 771s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '22' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 771s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '23' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 771s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '33' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 771s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '35' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 771s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '36' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 771s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '42' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 771s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '43' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 771s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '45' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 771s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '46' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 771s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '50' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 771s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '54' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 771s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '61' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 771s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '67' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 771s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '69' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 771s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '72' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 771s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '80' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 771s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '81' because it was < 2 characters long 771s Read 50 alignments... 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 771s Read 100 alignments... 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 771s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '82' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 771s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '83' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 771s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '84' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 771s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '99' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 771s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '104' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 771s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '105' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 771s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '106' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 771s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '110' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 771s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '111' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 771s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '114' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 771s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '115' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 771s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '116' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 771s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '118' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 771s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '119' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 771s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '124' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 771s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '127' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 771s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '128' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 771s Warning: skipping mate #2 of read '130' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '130' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 771s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '133' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 771s Warning: skipping mate #1 of read '134' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '134' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 771s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '139' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 771s Read 150 alignments... 771s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 771s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '148' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 771s Warning: skipping mate #1 of read '149' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '149' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 771s Warning: skipping mate #2 of read '150' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '150' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 771s Warning: skipping mate #2 of read '157' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '157' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 771s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '158' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 771s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '159' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 771s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '164' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 771s Warning: skipping mate #1 of read '166' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '166' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 771s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '167' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 771s Warning: skipping read '168' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '168' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 771s Warning: skipping mate #1 of read '169' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '169' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 771s Warning: skipping mate #2 of read '170' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '170' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 771s Read 200 alignments... 771s 174 reads; of these: 771s 129 (74.14%) were paired; of these: 771s 127 (98.45%) aligned concordantly 0 times 771s 0 (0.00%) aligned concordantly exactly 1 time 771s 2 (1.55%) aligned concordantly >1 times 771s ---- 771s 127 pairs aligned concordantly 0 times; of these: 771s 2 (1.57%) aligned discordantly 1 time 771s ---- 771s 125 pairs aligned 0 times concordantly or discordantly; of these: 771s 250 mates make up the pairs; of these: 771s 219 (87.60%) aligned 0 times 771s 28 (11.20%) aligned exactly 1 time 771s 3 (1.20%) aligned >1 times 771s 45 (25.86%) were unpaired; of these: 771s 39 (86.67%) aligned 0 times 771s 5 (11.11%) aligned exactly 1 time 771s 1 (2.22%) aligned >1 times 771s 14.85% overall alignment rate 771s Read 250 alignments... 771s Read 300 alignments... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AGTT 771s AGTT 771s Processing line... 771s Processing line... 771s CTCCTGAAA 771s CTCCTGAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TACCTCCTGAAAAC 771s TACCTCCTGAAAAC 771s Processing line... 771s AACGCAG 771s AACGCAG 771s Processing line... 771s Processing line... 771s Processing line... 771s TACCTCCTGAAAACAT 771s TACCTCCTGAAAACAT 771s Processing line... 771s Processing line... 771s CGCAGTTACCTCCTGAA 771s CGCAGTTACCTCCTGAA 771s Processing line... 771s Processing line... 771s ACCTCC 771s ACCTCC 771s Processing line... 771s Processing line... 771s TCCTGAA 771s TCCTGAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ATGAGTGATTAATAACGT 771s ATGAGTGATTAATAACGT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACAACGCAGTTACCTCCTGAAAA 771s ACAACGCAGTTACCTCCTGAAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GTGA 771s GTGA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GAA 771s GAA 771s Processing line... 771s GCAGT 771s GCAGT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CGCAGTT 771s CGCAGTT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TCCTGA 771s TCCTGA 771s Processing line... 771s Processing line... 771s Processing line... 771s GCAGT 771s GCAGT 771s Processing line... 771s Processing line... 771s CCT 771s CCT 771s Processing line... 771s Processing line... 771s GCAGTTACC 771s GCAGTTACC 771s Processing line... 771s Processing line... 771s Processing line... 771s AT 771s AT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TG 771s TG 771s Processing line... 771s AC 771s AC 771s Processing line... 771s Processing line... 771s Processing line... 771s ACGAC 771s ACGAC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACAACGCAGTTACCTCCTGAAAAC 771s ACAACGCAGTTACCTCCTGAAAAC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACGCAGTTA 771s ACGCAGTTA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACGCAGTTACCTCCTGAAAACATCC 771s ACGCAGTTACCTCCTGAAAACATCC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AACAACGCAGTTACCTCCTGA 771s AACAACGCAGTTACCTCCTGA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AACAACGCAGTTACCTC 771s AACAACGCAGTTACCTC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AAAA 771s AAAA 771s Processing line... 771s GTTA 771s GTTA 771s Processing line... 771s Processing line... 771s /usr/bin/bowtie2 -R 3 --cp-min 8 -i S,0.82744940339271,5.04024650828026 --trim5 5 -M 2 --np 3 --trim3 8 -N 0 -L19 --cp-ival 1 --rdg 44.2981916164729 --rfg 46.4732593960255,5.37773597897383 --score-min L,9.40683052576175,5.31927337177947 -f -p 2 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 771s Processing line... 771s GTTACCTCCTGAAAA 771s GTTACCTCCTGAAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACGCAGTTACCTCCTGAA 771s ACGCAGTTACCTCCTGAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GCAGTTA 771s GCAGTTA 771s Processing line... 771s Processing line... 771s AA 771s AA 771s Processing line... 771s CCT 771s CCT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GCAGTTACCTCC 771s GCAGTTACCTCC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TAATAAC 771s TAATAAC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GCAGTTAC 771s GCAGTTAC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GCAGTTACCTCCTGAAAA 771s GCAGTTACCTCCTGAAAA 771s Processing line... 771s CAGTTAC 771s CAGTTAC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AGTTACCTCCTGAAAA 771s AGTTACCTCCTGAAAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CGCAGTTACC 771s CGCAGTTACC 771s Processing line... 771s Processing line... 771s Processing line... 771s GATATGAGTGATTAA 771s GATATGAGTGATTAA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s ACAACGCAGTTACCT 771s ACAACGCAGTTACCT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CGCAGTTACCTCCTG 771s CGCAGTTACCTCCTG 771s Processing line... 771s Processing line... 771s Processing line... 771s CTCCTG 771s CTCCTG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s --- Summary --- 771s Read 1 reference strings 771s Checked 45 alignments, 0 edits 771s --------------- 771s PASSED 771s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 771s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 771s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '7' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 771s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '12' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 771s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '16' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 771s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '22' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 771s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '23' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 771s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 771s Warning: skipping read '33' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 771s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '35' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 771s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '36' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 771s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '42' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 771s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '43' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 771s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '45' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 771s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '46' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 771s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '50' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 771s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '54' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 771s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '61' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 771s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '67' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 771s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '69' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 771s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '72' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 771s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '80' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 771s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '81' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 771s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '82' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 771s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '83' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 771s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '84' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 771s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '99' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 771s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '104' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 771s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '105' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 771s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '106' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 771s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '110' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 771s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '111' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 771s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '114' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 771s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '115' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 771s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '116' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 771s Warning: skipping mate #1 of read '118' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '118' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 771s Warning: skipping mate #1 of read '119' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '119' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 771s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '124' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 771s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '127' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 771s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '128' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 771s Warning: skipping mate #2 of read '130' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '130' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 771s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '133' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 771s Warning: skipping mate #1 of read '134' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '134' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 771s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '139' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 771s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '148' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 771s Warning: skipping mate #1 of read '149' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '149' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 771s Warning: skipping mate #2 of read '150' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '150' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 771s Warning: skipping mate #2 of read '157' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '157' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 771s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '158' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 771s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '159' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 771s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '164' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 771s Warning: skipping mate #1 of read '166' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '166' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 771s Warning: skipping mate #1 of read '167' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '167' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 771s Warning: skipping read '168' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '168' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 771s Warning: skipping mate #1 of read '169' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '169' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 771s Warning: skipping mate #2 of read '170' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '170' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 771s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 771s 174 reads; of these: 771s 129 (74.14%) were paired; of these: 771s 127 (98.45%) aligned concordantly 0 times 771s 0 (0.00%) aligned concordantly exactly 1 time 771s 2 (1.55%) aligned concordantly >1 times 771s ---- 771s 127 pairs aligned concordantly 0 times; of these: 771s 2 (1.57%) aligned discordantly 1 time 771s ---- 771s 125 pairs aligned 0 times concordantly or discordantly; of these: 771s 250 mates make up the pairs; of these: 771s 219 (87.60%) aligned 0 times 771s 28 (11.20%) aligned exactly 1 time 771s 3 (1.20%) aligned >1 times 771s 45 (25.86%) were unpaired; of these: 771s 39 (86.67%) aligned 0 times 771s 5 (11.11%) aligned exactly 1 time 771s 1 (2.22%) aligned >1 times 771s 14.85% overall alignment rate 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.2 771s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.1 771s Introducing 3 SNPs, 2/0 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 6 771s Reference gaps introduced: 2 771s Read gaps introduced: 1 771s Rearrangements introduced: 0 771s Created read sampler 771s Sampling 74 reads 771s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 771s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 74 reference bases 771s *** Run 45 of 100 771s /usr/bin/bowtie2 -a -i S,2.842241266086,4.9826360999253 --trim5 7 --score-min L,9.66142750029515,5.94914075996586 --rdg 3.06342995697239,1.28318680267356 --np 2 --mp 1.32353220065135,1.19072280880596 -N 0 -L23 --cp-min 3 --cp-ival 1 --qseq -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 771s 74 reads; of these: 771s 74 (100.00%) were unpaired; of these: 771s 63 (85.14%) aligned 0 times 771s 6 (8.11%) aligned exactly 1 time 771s 5 (6.76%) aligned >1 times 771s 14.86% overall alignment rate 771s Read 50 alignments... 771s Read 100 alignments... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s /usr/bin/bowtie2 -a -i S,2.842241266086,4.9826360999253 --trim5 7 --score-min L,9.66142750029515,5.94914075996586 --rdg 3.06342995697239,1.28318680267356 --np 2 --mp 1.32353220065135,1.19072280880596 -N 0 -L23 --cp-min 3 --cp-ival 1 --qseq -p 3 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AC 771s AC 771s Processing line... 771s AC 771s AC 771s Processing line... 771s GT 771s GT 771s Processing line... 771s AC 771s AC 771s Processing line... 771s AC 771s AC 771s Processing line... 771s GT 771s GT 771s Processing line... 771s AC 771s AC 771s Processing line... 771s GT 771s GT 771s Processing line... 771s AC 771s AC 771s Processing line... 771s AC 771s AC 771s Processing line... 771s AC 771s AC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s GTTA 771s GTTA 771s Processing line... 771s TAAC 771s TAAC 771s Processing line... 771s TAAC 771s TAAC 771s Processing line... 771s CTGAAAACA 771s CTGAAAACA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TATGAGTGATT 771s TATGAGTGATT 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TCCTGAA 771s TCCTGAA 771s Processing line... 771s TAATAACGT 771s TAATAACGT 771s Processing line... 771s Processing line... 771s AGT 771s AGT 771s Processing line... 771s AGT 771s AGT 771s Processing line... 771s Processing line... 771s GTTACCTCCTG 771s GTTACCTCCTG 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s TT 771s TT 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s AA 771s AA 771s Processing line... 771s TT 771s TT 771s Processing line... 771s AA 771s AA 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s CATC 771s CATC 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s Processing line... 771s TCC 771s TCC 771s Processing line... 771s TCC 771s TCC 771s --- Summary --- 771s Read 1 reference strings 771s Checked 34 alignments, 0 edits 771s --------------- 771s PASSED 771s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 771s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 771s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 771s 74 reads; of these: 771s 74 (100.00%) were unpaired; of these: 771s 63 (85.14%) aligned 0 times 771s 6 (8.11%) aligned exactly 1 time 771s 5 (6.76%) aligned >1 times 771s 14.86% overall alignment rate 771s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 771s Flattened IUPAC characters 771s Mutating sequence Sim.pm.2 771s Introducing 7 SNPs, 0/2 ref/read gaps, and 0 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutating sequence Sim.pm.1 771s Introducing 3 SNPs, 0/1 ref/read gaps, and 1 rearrangements 771s Finished SNPs 771s Finished ref gaps 771s Finished read gaps 771s Mutated reference genome to subject genome 771s SNPs introduced: 10 771s Reference gaps introduced: 0 771s Read gaps introduced: 3 771s Rearrangements introduced: 1 771s Created read sampler 771s Sampling 209 reads 771s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 771s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 771s *** Run 46 of 100 771s /usr/bin/bowtie2 --ma 36.6293079524726 --cp-min 3 --cp-ival 2 --n-ceil 0.722679343040914,0.210137144132358 --trim5 6 --score-min L,5.721869679335,6.08246917603998 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 771s parsing sequence Sim.pm.1... 771s parsing sequence Sim.pm.2... 771s Parsed 74 reference bases 771s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 771s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '2' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 771s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '9' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 771s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '15' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 771s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '20' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 771s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '25' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 771s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '29' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 771s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 771s Warning: skipping read '35' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 771s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '39' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 771s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '44' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 771s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '45' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 771s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '48' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 771s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '50' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 771s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 771s Warning: skipping mate #1 of read '53' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 771s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 771s Warning: skipping mate #2 of read '56' because it was < 2 characters long 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 771s Read 50 alignments... 771s Read 100 alignments... 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 771s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 772s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '69' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 772s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '76' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 772s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '82' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 772s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '87' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 772s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '91' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 772s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '100' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 772s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '109' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 772s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '114' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 772s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '115' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 772s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '118' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 772s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '132' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 772s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '133' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 772s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '137' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 772s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '143' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 772s Warning: skipping mate #2 of read '145' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '145' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 772s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '158' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 772s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '180' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 772s Read 150 alignments... 772s Read 200 alignments... 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '201; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 772s Warning: skipping mate #1 of read '202' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '202' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 772s Warning: skipping mate #1 of read '205' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '205' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 772s Warning: skipping mate #1 of read '206' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '206' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 772s Warning: skipping mate #1 of read '207' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '207' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 772s Read 250 alignments... 772s Read 300 alignments... 772s 209 reads; of these: 772s 185 (88.52%) were paired; of these: 772s 183 (98.92%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 2 (1.08%) aligned concordantly >1 times 772s ---- 772s 183 pairs aligned concordantly 0 times; of these: 772s 1 (0.55%) aligned discordantly 1 time 772s ---- 772s 182 pairs aligned 0 times concordantly or discordantly; of these: 772s 364 mates make up the pairs; of these: 772s 328 (90.11%) aligned 0 times 772s 20 (5.49%) aligned exactly 1 time 772s 16 (4.40%) aligned >1 times 772s 24 (11.48%) were unpaired; of these: 772s 24 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 10.66% overall alignment rate 772s Read 350 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TGAAA 772s TGAAA 772s Processing line... 772s Processing line... 772s Processing line... 772s CG 772s CG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CCTCCTGAAA 772s CCTCCTGAAA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CAACGCAGT 772s CAACGCAGT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TGAA 772s TGAA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CCTGAAAACATC 772s CCTGAAAACATC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GAC 772s GAC 772s Processing line... 772s AT 772s AT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CCTCCTGAAAACATC 772s CCTCCTGAAAACATC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GA 772s GA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TGA 772s TGA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AC 772s AC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s /usr/bin/bowtie2 --ma 36.6293079524726 --cp-min 3 --cp-ival 2 --n-ceil 0.722679343040914,0.210137144132358 --trim5 6 --score-min L,5.721869679335,6.08246917603998 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CTCCTGAAA 772s CTCCTGAAA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CCTGAAAACAT 772s CCTGAAAACAT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AGATAT 772s AGATAT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AA 772s AA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AC 772s AC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TGAAAACAT 772s TGAAAACAT 772s Processing line... 772s Processing line... 772s AG 772s AG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TCT 772s TCT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AA 772s AA 772s Processing line... 772s GAC 772s GAC 772s Processing line... 772s Processing line... 772s Processing line... 772s CGCAG 772s CGCAG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CCGAGA 772s CCGAGA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CCTCCTGAA 772s CCTCCTGAA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AC 772s AC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s ATAGACG 772s ATAGACG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TG 772s TG 772s Processing line... 772s Processing line... 772s AC 772s AC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AGAT 772s AGAT 772s Processing line... 772s Processing line... 772s AC 772s AC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s ACGC 772s ACGC 772s Processing line... 772s CGTC 772s CGTC 772s Processing line... 772s Processing line... 772s Processing line... 772s ATA 772s ATA 772s Processing line... 772s Processing line... 772s ACGCAG 772s ACGCAG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AACGC 772s AACGC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CCTGAAA 772s CCTGAAA 772s Processing line... 772s Processing line... 772s CCTCCTGA 772s CCTCCTGA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AACGCA 772s AACGCA 772s Processing line... 772s TGAA 772s TGAA 772s Processing line... 772s TAAC 772s TAAC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s ATG 772s ATG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 42 alignments, 0 edits 772s --------------- 772s PASSED 772s ALSO checking that bowtie2 and bowtie2-align match up 772s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 772s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '2' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 772s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '9' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '15' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 772s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '20' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 772s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '25' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 772s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '29' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '35' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 772s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '39' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 772s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '44' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 772s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '45' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 772s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '48' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 772s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '50' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 772s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '53' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 772s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '56' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 772s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '69' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 772s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '76' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 772s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '82' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 772s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '87' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 772s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '91' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 772s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '100' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 772s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '109' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 772s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '114' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 772s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '115' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 772s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '118' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 772s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '132' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 772s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '133' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 772s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '137' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 772s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '143' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 772s Warning: skipping mate #2 of read '145' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '145' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 772s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '158' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 772s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '180' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 772s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 772s /usr/bin/bowtie2 --ma 36.6293079524726 --cp-min 3 --cp-ival 2 --n-ceil 0.722679343040914,0.210137144132358 --trim5 6 --score-min L,5.721869679335,6.08246917603998 -r -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '201; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 772s Warning: skipping mate #1 of read '202' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '202' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 772s Warning: skipping mate #1 of read '205' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '205' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 772s Warning: skipping mate #1 of read '206' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '206' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 772s Warning: skipping mate #1 of read '207' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '207' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 772s 209 reads; of these: 772s 185 (88.52%) were paired; of these: 772s 183 (98.92%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 2 (1.08%) aligned concordantly >1 times 772s ---- 772s 183 pairs aligned concordantly 0 times; of these: 772s 1 (0.55%) aligned discordantly 1 time 772s ---- 772s 182 pairs aligned 0 times concordantly or discordantly; of these: 772s 364 mates make up the pairs; of these: 772s 328 (90.11%) aligned 0 times 772s 20 (5.49%) aligned exactly 1 time 772s 16 (4.40%) aligned >1 times 772s 24 (11.48%) were unpaired; of these: 772s 24 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 10.66% overall alignment rate 772s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 772s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 772s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '2' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 772s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '9' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '15' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 772s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '20' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 772s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '25' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 772s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '29' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '35' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 772s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '39' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 772s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '44' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 772s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '45' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 772s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '48' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 772s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '50' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 772s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '53' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 772s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '56' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 772s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '69' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 772s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '76' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 772s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '82' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 772s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '87' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 772s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '91' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 772s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '100' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 772s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '109' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 772s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '114' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 772s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '115' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 772s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '118' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 772s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '132' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 772s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '133' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 772s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '137' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 772s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '143' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 772s Warning: skipping mate #2 of read '145' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '145' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 772s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '158' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 772s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '180' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '201; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 772s Warning: skipping mate #1 of read '202' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '202' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 772s Warning: skipping mate #1 of read '205' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '205' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 772s Warning: skipping mate #1 of read '206' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '206' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 772s Warning: skipping mate #1 of read '207' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '207' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 772s 209 reads; of these: 772s 185 (88.52%) were paired; of these: 772s 183 (98.92%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 2 (1.08%) aligned concordantly >1 times 772s ---- 772s 183 pairs aligned concordantly 0 times; of these: 772s 1 (0.55%) aligned discordantly 1 time 772s ---- 772s 182 pairs aligned 0 times concordantly or discordantly; of these: 772s 364 mates make up the pairs; of these: 772s 328 (90.11%) aligned 0 times 772s 20 (5.49%) aligned exactly 1 time 772s 16 (4.40%) aligned >1 times 772s 24 (11.48%) were unpaired; of these: 772s 24 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 10.66% overall alignment rate 772s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 772s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 772s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 772s /usr/bin/bowtie2 --ma 36.6293079524726 --cp-min 3 --cp-ival 2 --n-ceil 0.722679343040914,0.210137144132358 --trim5 6 --score-min L,5.721869679335,6.08246917603998 -r -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 772s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 772s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 772s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '2' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 772s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '9' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '15' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 772s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '20' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 772s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '25' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 772s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '29' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '35' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 772s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '39' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 772s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '44' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 772s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '45' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 772s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '48' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 772s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '50' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 772s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '53' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 772s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '56' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 772s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '69' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 772s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '76' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 772s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '82' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 772s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '87' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 772s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '91' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 772s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '100' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 772s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '109' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 772s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '114' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 772s Warning: skipping mate #1 of read '115' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '115' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 772s Warning: skipping mate #1 of read '118' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '118' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 772s Warning: skipping mate #1 of read '132' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '132' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 772s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '133' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 772s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '137' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 772s Warning: skipping mate #1 of read '143' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '143' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 772s Warning: skipping mate #2 of read '145' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '145' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 772s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '158' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 772s Warning: skipping mate #1 of read '180' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '180' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '201; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 772s Warning: skipping mate #1 of read '202' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '202' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 772s Warning: skipping mate #1 of read '205' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '205' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 772s Warning: skipping mate #1 of read '206' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '206' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 772s Warning: skipping mate #1 of read '207' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '207' because it was < 2 characters long 772s 209 reads; of these: 772s 185 (88.52%) were paired; of these: 772s 183 (98.92%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 2 (1.08%) aligned concordantly >1 times 772s ---- 772s 183 pairs aligned concordantly 0 times; of these: 772s 1 (0.55%) aligned discordantly 1 time 772s ---- 772s 182 pairs aligned 0 times concordantly or discordantly; of these: 772s 364 mates make up the pairs; of these: 772s 328 (90.11%) aligned 0 times 772s 20 (5.49%) aligned exactly 1 time 772s 16 (4.40%) aligned >1 times 772s 24 (11.48%) were unpaired; of these: 772s 24 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 10.66% overall alignment rate 772s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.1 772s Introducing 2 SNPs, 1/2 ref/read gaps, and 1 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.2 772s Introducing 3 SNPs, 0/1 ref/read gaps, and 1 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 5 772s Reference gaps introduced: 1 772s Read gaps introduced: 3 772s Rearrangements introduced: 2 772s Created read sampler 772s Sampling 46 reads 772s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 772s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s Parsed 74 reference bases 772s *** Run 47 of 100 772s /usr/bin/bowtie2 --trim3 5 --local --cp-ival 1 --mp 6.5222840352888,4.8028319008838 -a --rfg 35.797180780098 --rdg 35.2272579312869 --score-min L,5.57712985484676,2.55096812910973 --cp-min 8 -i S,2.44583264873166 --np 2 --norc -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 772s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '14' because it was < 2 characters long 772s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '23' because it was < 2 characters long 772s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '28' because it was < 2 characters long 772s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '29' because it was < 2 characters long 772s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '44' because it was < 2 characters long 772s 46 reads; of these: 772s 38 (82.61%) were paired; of these: 772s 38 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 38 pairs aligned concordantly 0 times; of these: 772s 0 (0.00%) aligned discordantly 1 time 772s ---- 772s 38 pairs aligned 0 times concordantly or discordantly; of these: 772s 76 mates make up the pairs; of these: 772s 76 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 8 (17.39%) were unpaired; of these: 772s 8 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s Read 50 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 0 alignments, 0 edits 772s --------------- 772s PASSED 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.2 772s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.1 772s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 6 772s Reference gaps introduced: 1 772s Read gaps introduced: 0 772s Rearrangements introduced: 1 772s Created read sampler 772s Sampling 117 reads 772s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 772s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s *** Run 48 of 100 772s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --ma 37.5614858957596 -N 0 -L29 --mp 7.70341415879792,2.26540813481421 --mm -M 6 --np 3 --gbar 3 --score-min L,8.21595299027674,5.51197754522697 --rdg 24.4378868887296,9.21360199300394 --rfg 29.7481552369861,3.05263308923403 -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw 772s Parsed 74 reference bases 772s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 772s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 772s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 772s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '27' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 772s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '43' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 772s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '47' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 772s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '50' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 772s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '109' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 772s 117 reads; of these: 772s 117 (100.00%) were unpaired; of these: 772s 89 (76.07%) aligned 0 times 772s 15 (12.82%) aligned exactly 1 time 772s 13 (11.11%) aligned >1 times 772s 23.93% overall alignment rate 772s Read 50 alignments... 772s Read 100 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s /usr/bin/bowtie2 --cp-min 5 --cp-ival 1 --ma 37.5614858957596 -N 0 -L29 --mp 7.70341415879792,2.26540813481421 --mm -M 6 --np 3 --gbar 3 --score-min L,8.21595299027674,5.51197754522697 --rdg 24.4378868887296,9.21360199300394 --rfg 29.7481552369861,3.05263308923403 -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 772s Processing line... 772s Processing line... 772s TATGAGTG 772s TATGAGTG 772s Processing line... 772s Processing line... 772s TTACCTCCT 772s TTACCTCCT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AGTT 772s AGTT 772s Processing line... 772s CC 772s CC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TG 772s TG 772s Processing line... 772s Processing line... 772s CG 772s CG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CTGAAAACATCC 772s CTGAAAACATCC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CTGAAAA 772s CTGAAAA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AACCGAGA 772s AACCGAGA 772s Processing line... 772s Processing line... 772s Processing line... 772s ACCGAGATATGAGTGATTAATAAC 772s ACCGAGATATGAGTGATTAATAAC 772s Processing line... 772s Processing line... 772s Processing line... 772s GAA 772s GAA 772s Processing line... 772s Processing line... 772s GAT 772s GAT 772s Processing line... 772s GAAAACA 772s GAAAACA 772s Processing line... 772s Processing line... 772s CA 772s CA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AACGCA 772s AACGCA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GATTAATAAC 772s GATTAATAAC 772s Processing line... 772s AAC 772s AAC 772s Processing line... 772s Processing line... 772s AG 772s AG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AAAACA 772s AAAACA 772s Processing line... 772s Processing line... 772s CCT 772s CCT 772s Processing line... 772s Processing line... 772s Processing line... 772s TGA 772s TGA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TGA 772s TGA 772s Processing line... 772s Processing line... 772s Processing line... 772s TGA 772s TGA 772s Processing line... 772s AGT 772s AGT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AACAACGCAGT 772s AACAACGCAGT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AA 772s AA 772s Processing line... 772s Processing line... 772s TTACCTC 772s TTACCTC 772s Processing line... 772s Processing line... 772s AAAACA 772s AAAACA 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 28 alignments, 0 edits 772s --------------- 772s PASSED 772s ALSO checking that bowtie2 and bowtie2-align match up 772s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 772s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 772s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 772s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '27' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 772s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '43' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 772s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '47' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 772s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '50' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 772s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 772s Warning: skipping read '109' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 772s 117 reads; of these: 772s 117 (100.00%) were unpaired; of these: 772s 89 (76.07%) aligned 0 times 772s 15 (12.82%) aligned exactly 1 time 772s 13 (11.11%) aligned >1 times 772s 23.93% overall alignment rate 772s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.1 772s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.2 772s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 6 772s Reference gaps introduced: 0 772s Read gaps introduced: 1 772s Rearrangements introduced: 0 772s Created read sampler 772s Sampling 78 reads 772s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 772s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s Parsed 74 reference bases 772s *** Run 49 of 100 772s /usr/bin/bowtie2 -k 4 --trim5 9 --np 1 -R 4 --cp-min 9 --ma 22.6285475862336 --mm --score-min L,3.96518975637906,5.15449744934788 --trim3 1 --cp-ival 2 --n-ceil 0.167586570253996,0.0579079351956837 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 772s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 772s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 772s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '2' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 772s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '7' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 772s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '14' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '15' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 772s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '24' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 772s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '27' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 772s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '30' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 772s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '32' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 772s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '40' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 772s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '43' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 772s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '44' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 772s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '50' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 772s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '61' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 772s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '62' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 772s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '74' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 772s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '76' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 772s 78 reads; of these: 772s 58 (74.36%) were paired; of these: 772s 58 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 58 pairs aligned concordantly 0 times; of these: 772s 1 (1.72%) aligned discordantly 1 time 772s ---- 772s 57 pairs aligned 0 times concordantly or discordantly; of these: 772s 114 mates make up the pairs; of these: 772s 101 (88.60%) aligned 0 times 772s 10 (8.77%) aligned exactly 1 time 772s 3 (2.63%) aligned >1 times 772s 20 (25.64%) were unpaired; of these: 772s 15 (75.00%) aligned 0 times 772s 4 (20.00%) aligned exactly 1 time 772s 1 (5.00%) aligned >1 times 772s 14.71% overall alignment rate 772s Read 50 alignments... 772s Read 100 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s ATAGACGA 772s ATAGACGA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GCAGTTACCTCCTGA 772s GCAGTTACCTCCTGA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CAT 772s CAT 772s Processing line... 772s ATG 772s ATG 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AATA 772s AATA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CTCCTGAA 772s CTCCTGAA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s ACCTCCTGAAAACAT 772s ACCTCCTGAAAACAT 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s CATC 772s CATC 772s Processing line... 772s Processing line... 772s AAAA 772s AAAA 772s Processing line... 772s GTTACCTCCTGAAAACA 772s GTTACCTCCTGAAAACA 772s Processing line... 772s Processing line... 772s AACGC 772s AACGC 772s Processing line... 772s AATA 772s AATA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s AGTTACCTCC 772s AGTTACCTCC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s TGAAA 772s TGAAA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s /usr/bin/bowtie2 -k 4 --trim5 9 --np 1 -R 4 --cp-min 9 --ma 22.6285475862336 --mm --score-min L,3.96518975637906,5.15449744934788 --trim3 1 --cp-ival 2 --n-ceil 0.167586570253996,0.0579079351956837 -f -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 772s AATAAC 772s AATAAC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GCAGTTACCTCC 772s GCAGTTACCTCC 772s Processing line... 772s Processing line... 772s CGA 772s CGA 772s Processing line... 772s CGA 772s CGA 772s Processing line... 772s CAGTTACCTCCTGAAAACATC 772s CAGTTACCTCCTGAAAACATC 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s GA 772s GA 772s Processing line... 772s GA 772s GA 772s Processing line... 772s GA 772s GA 772s Processing line... 772s GA 772s GA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s ATAGACGA 772s ATAGACGA 772s Processing line... 772s CA 772s CA 772s Processing line... 772s CA 772s CA 772s Processing line... 772s CA 772s CA 772s Processing line... 772s CA 772s CA 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 28 alignments, 0 edits 772s --------------- 772s PASSED 772s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 772s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 772s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 772s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '2' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 772s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '7' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 772s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '14' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '15' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 772s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '24' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 772s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '27' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 772s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '30' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 772s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '32' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 772s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '40' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 772s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '43' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 772s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '44' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 772s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '50' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 772s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '61' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 772s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '62' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 772s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '74' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 772s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '76' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 772s 78 reads; of these: 772s 58 (74.36%) were paired; of these: 772s 58 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 58 pairs aligned concordantly 0 times; of these: 772s 1 (1.72%) aligned discordantly 1 time 772s ---- 772s 57 pairs aligned 0 times concordantly or discordantly; of these: 772s 114 mates make up the pairs; of these: 772s 101 (88.60%) aligned 0 times 772s 10 (8.77%) aligned exactly 1 time 772s 3 (2.63%) aligned >1 times 772s 20 (25.64%) were unpaired; of these: 772s 15 (75.00%) aligned 0 times 772s 4 (20.00%) aligned exactly 1 time 772s 1 (5.00%) aligned >1 times 772s 14.71% overall alignment rate 772s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 772s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 772s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 772s /usr/bin/bowtie2 -k 4 --trim5 9 --np 1 -R 4 --cp-min 9 --ma 22.6285475862336 --mm --score-min L,3.96518975637906,5.15449744934788 --trim3 1 --cp-ival 2 --n-ceil 0.167586570253996,0.0579079351956837 -f -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 772s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 772s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 772s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 772s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '2' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 772s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '7' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 772s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '14' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 772s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '15' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 772s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '24' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 772s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '27' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 772s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '30' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 772s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '32' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 772s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '40' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 772s Warning: skipping mate #1 of read '43' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '43' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 772s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '44' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 772s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '50' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 772s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '61' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 772s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '62' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 772s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '74' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 772s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '76' because it was < 2 characters long 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 772s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 772s 78 reads; of these: 772s 58 (74.36%) were paired; of these: 772s 58 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 58 pairs aligned concordantly 0 times; of these: 772s 1 (1.72%) aligned discordantly 1 time 772s ---- 772s 57 pairs aligned 0 times concordantly or discordantly; of these: 772s 114 mates make up the pairs; of these: 772s 101 (88.60%) aligned 0 times 772s 10 (8.77%) aligned exactly 1 time 772s 3 (2.63%) aligned >1 times 772s 20 (25.64%) were unpaired; of these: 772s 15 (75.00%) aligned 0 times 772s 4 (20.00%) aligned exactly 1 time 772s 1 (5.00%) aligned >1 times 772s 14.71% overall alignment rate 772s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.1 772s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.2 772s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 0 772s Reference gaps introduced: 1 772s Read gaps introduced: 0 772s Rearrangements introduced: 1 772s Created read sampler 772s Sampling 53 reads 772s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 772s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s *** Run 50 of 100 772s /usr/bin/bowtie2 -k 2 --np 2 --cp-min 5 --score-min L,3.23928535512614,7.76513391129504 --trim3 8 --cp-ival 3 --local --mp 6.69741481462506,4.69539902364319 --nofw -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 772s Parsed 74 reference bases 772s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '9' because it was < 2 characters long 772s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '11' because it was < 2 characters long 772s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '12' because it was < 2 characters long 772s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '19' because it was < 2 characters long 772s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '23' because it was < 2 characters long 772s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '26' because it was < 2 characters long 772s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '27' because it was < 2 characters long 772s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '32' because it was < 2 characters long 772s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '39' because it was < 2 characters long 772s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '46' because it was < 2 characters long 772s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '50' because it was < 2 characters long 772s 53 reads; of these: 772s 38 (71.70%) were paired; of these: 772s 38 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 38 pairs aligned concordantly 0 times; of these: 772s 0 (0.00%) aligned discordantly 1 time 772s ---- 772s 38 pairs aligned 0 times concordantly or discordantly; of these: 772s 76 mates make up the pairs; of these: 772s 76 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 15 (28.30%) were unpaired; of these: 772s 15 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s Read 50 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 0 alignments, 0 edits 772s --------------- 772s PASSED 772s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 772s /usr/bin/bowtie2 -k 2 --np 2 --cp-min 5 --score-min L,3.23928535512614,7.76513391129504 --trim3 8 --cp-ival 3 --local --mp 6.69741481462506,4.69539902364319 --nofw -r -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 772s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '9' because it was < 2 characters long 772s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '11' because it was < 2 characters long 772s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '12' because it was < 2 characters long 772s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '19' because it was < 2 characters long 772s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '23' because it was < 2 characters long 772s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '26' because it was < 2 characters long 772s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '27' because it was < 2 characters long 772s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '32' because it was < 2 characters long 772s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '39' because it was < 2 characters long 772s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '46' because it was < 2 characters long 772s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '50' because it was < 2 characters long 772s 53 reads; of these: 772s 38 (71.70%) were paired; of these: 772s 38 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 38 pairs aligned concordantly 0 times; of these: 772s 0 (0.00%) aligned discordantly 1 time 772s ---- 772s 38 pairs aligned 0 times concordantly or discordantly; of these: 772s 76 mates make up the pairs; of these: 772s 76 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 15 (28.30%) were unpaired; of these: 772s 15 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.1 772s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.2 772s Introducing 5 SNPs, 0/0 ref/read gaps, and 2 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 6 772s Reference gaps introduced: 0 772s Read gaps introduced: 1 772s Rearrangements introduced: 2 772s Created read sampler 772s Sampling 46 reads 772s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 772s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 772s *** Run 51 of 100 772s /usr/bin/bowtie2 --cp-min 3 -k 5 --trim3 2 --nofw --mp 8.40818291143307,1.38399142382633 --cp-ival 1 --local --score-min L,6.77717583070507,7.3474160714682 --rfg 2.94363078251882 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s Parsed 74 reference bases 772s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '2' because it was < 2 characters long 772s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 772s Warning: skipping read '3' because it was < 2 characters long 772s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '6' because it was < 2 characters long 772s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '37' because it was < 2 characters long 772s 46 reads; of these: 772s 45 (97.83%) were paired; of these: 772s 45 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 45 pairs aligned concordantly 0 times; of these: 772s 0 (0.00%) aligned discordantly 1 time 772s ---- 772s 45 pairs aligned 0 times concordantly or discordantly; of these: 772s 90 mates make up the pairs; of these: 772s 90 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 1 (2.17%) were unpaired; of these: 772s 1 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s Read 50 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 0 alignments, 0 edits 772s --------------- 772s PASSED 772s Flattened IUPAC characters 772s Mutating sequence Sim.pm.1 772s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutating sequence Sim.pm.2 772s Introducing 3 SNPs, 4/0 ref/read gaps, and 0 rearrangements 772s Finished SNPs 772s Finished ref gaps 772s Finished read gaps 772s Mutated reference genome to subject genome 772s SNPs introduced: 4 772s Reference gaps introduced: 4 772s Read gaps introduced: 1 772s Rearrangements introduced: 1 772s Created read sampler 772s Sampling 60 reads 772s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 772s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 772s parsing sequence Sim.pm.1... 772s parsing sequence Sim.pm.2... 772s Parsed 74 reference bases 772s *** Run 52 of 100 772s /usr/bin/bowtie2 --mm --score-min L,1.17901701536795,3.09661510224095 --rdg 47.3596336262156,2.05111660498423 --mp 8.28790199266359,3.21847682286544 -N 0 -L15 --cp-ival 1 --local --trim5 2 --norc --cp-min 3 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 772s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 772s Warning: skipping mate #1 of read '12' because it was < 2 characters long 772s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 772s Warning: skipping mate #2 of read '33' because it was < 2 characters long 772s 60 reads; of these: 772s 55 (91.67%) were paired; of these: 772s 55 (100.00%) aligned concordantly 0 times 772s 0 (0.00%) aligned concordantly exactly 1 time 772s 0 (0.00%) aligned concordantly >1 times 772s ---- 772s 55 pairs aligned concordantly 0 times; of these: 772s 0 (0.00%) aligned discordantly 1 time 772s ---- 772s 55 pairs aligned 0 times concordantly or discordantly; of these: 772s 110 mates make up the pairs; of these: 772s 110 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 5 (8.33%) were unpaired; of these: 772s 5 (100.00%) aligned 0 times 772s 0 (0.00%) aligned exactly 1 time 772s 0 (0.00%) aligned >1 times 772s 0.00% overall alignment rate 772s Read 50 alignments... 772s Read 100 alignments... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s Processing line... 772s --- Summary --- 772s Read 1 reference strings 772s Checked 0 alignments, 0 edits 772s --------------- 772s PASSED 772s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 772s /usr/bin/bowtie2 --mm --score-min L,1.17901701536795,3.09661510224095 --rdg 47.3596336262156,2.05111660498423 --mp 8.28790199266359,3.21847682286544 -N 0 -L15 --cp-ival 1 --local --trim5 2 --norc --cp-min 3 -q -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 773s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '12' because it was < 2 characters long 773s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '33' because it was < 2 characters long 773s 60 reads; of these: 773s 55 (91.67%) were paired; of these: 773s 55 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 55 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 55 pairs aligned 0 times concordantly or discordantly; of these: 773s 110 mates make up the pairs; of these: 773s 110 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 5 (8.33%) were unpaired; of these: 773s 5 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 773s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 773s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.2 773s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.1 773s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 10 773s Reference gaps introduced: 1 773s Read gaps introduced: 0 773s Rearrangements introduced: 1 773s Created read sampler 773s Sampling 105 reads 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 773s *** Run 53 of 100 773s /usr/bin/bowtie2 --score-min L,2.74782381326194,7.60936604989512 --rfg 44.8034017292267 --cp-ival 1 --local --nofw -N 0 -L29 --mp 9.28224207972669,7.66099114072707 --trim5 9 --np 4 -R 1 --cp-min 2 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '4' because it was < 2 characters long 773s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '7' because it was < 2 characters long 773s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '8' because it was < 2 characters long 773s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '9' because it was < 2 characters long 773s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '14' because it was < 2 characters long 773s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '17' because it was < 2 characters long 773s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '21' because it was < 2 characters long 773s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '22' because it was < 2 characters long 773s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '23' because it was < 2 characters long 773s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '33' because it was < 2 characters long 773s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '37' because it was < 2 characters long 773s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '38' because it was < 2 characters long 773s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '39' because it was < 2 characters long 773s Warning: skipping mate #2 of read '39' because it was < 2 characters long 773s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '40' because it was < 2 characters long 773s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '41' because it was < 2 characters long 773s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '54' because it was < 2 characters long 773s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '55' because it was < 2 characters long 773s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '56' because it was < 2 characters long 773s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 773s Read 50 alignments... 773s Read 100 alignments... 773s Warning: skipping mate #1 of read '86' because it was < 2 characters long 773s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '91' because it was < 2 characters long 773s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '96' because it was < 2 characters long 773s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '100' because it was < 2 characters long 773s Warning: skipping mate #1 of read '102' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '102' because it was < 2 characters long 773s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '104' because it was < 2 characters long 773s 105 reads; of these: 773s 79 (75.24%) were paired; of these: 773s 79 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 79 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 79 pairs aligned 0 times concordantly or discordantly; of these: 773s 158 mates make up the pairs; of these: 773s 158 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 26 (24.76%) were unpaired; of these: 773s 26 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s Read 150 alignments... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 0 alignments, 0 edits 773s --------------- 773s PASSED 773s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 773s /usr/bin/bowtie2 --score-min L,2.74782381326194,7.60936604989512 --rfg 44.8034017292267 --cp-ival 1 --local --nofw -N 0 -L29 --mp 9.28224207972669,7.66099114072707 --trim5 9 --np 4 -R 1 --cp-min 2 -q -p 4 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 773s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '4' because it was < 2 characters long 773s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '7' because it was < 2 characters long 773s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '8' because it was < 2 characters long 773s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '9' because it was < 2 characters long 773s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '14' because it was < 2 characters long 773s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '17' because it was < 2 characters long 773s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '21' because it was < 2 characters long 773s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '22' because it was < 2 characters long 773s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '23' because it was < 2 characters long 773s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '33' because it was < 2 characters long 773s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '37' because it was < 2 characters long 773s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '38' because it was < 2 characters long 773s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '39' because it was < 2 characters long 773s Warning: skipping mate #2 of read '39' because it was < 2 characters long 773s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '40' because it was < 2 characters long 773s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '41' because it was < 2 characters long 773s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '54' because it was < 2 characters long 773s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '55' because it was < 2 characters long 773s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '56' because it was < 2 characters long 773s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '86' because it was < 2 characters long 773s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '91' because it was < 2 characters long 773s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '96' because it was < 2 characters long 773s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '100' because it was < 2 characters long 773s Warning: skipping mate #1 of read '102' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '102' because it was < 2 characters long 773s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '104' because it was < 2 characters long 773s 105 reads; of these: 773s 79 (75.24%) were paired; of these: 773s 79 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 79 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 79 pairs aligned 0 times concordantly or discordantly; of these: 773s 158 mates make up the pairs; of these: 773s 158 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 26 (24.76%) were unpaired; of these: 773s 26 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.1 773s Introducing 4 SNPs, 2/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.2 773s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 4 773s Reference gaps introduced: 2 773s Read gaps introduced: 0 773s Rearrangements introduced: 1 773s Created read sampler 773s Sampling 70 reads 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s *** Run 54 of 100 773s /usr/bin/bowtie2 --mp 4.64583185775937,2.56239093272166 --cp-ival 1 --n-ceil 0.0786984093437739,1.29616400561013 -D 32 -a --score-min L,5.35546797756794,5.68414758478876 --rfg 41.6501502437809,3.70691305496153 --rdg 14.492672676629 --gbar 5 -R 3 --ma 24.1063557597996 --cp-min 2 --trim5 1 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 773s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 773s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 773s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '5' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 773s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '6' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 773s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '9' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 773s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '20' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 773s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '22' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 773s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '28' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 773s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '59' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 773s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '68' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 773s 70 reads; of these: 773s 70 (100.00%) were unpaired; of these: 773s 57 (81.43%) aligned 0 times 773s 12 (17.14%) aligned exactly 1 time 773s 1 (1.43%) aligned >1 times 773s 18.57% overall alignment rate 773s Read 50 alignments... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s ACAACGCAGTTACCTCCTGA 773s ACAACGCAGTTACCTCCTGA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GAGT 773s GAGT 773s Processing line... 773s CGC 773s CGC 773s Processing line... 773s Processing line... 773s Processing line... 773s CAACGC 773s CAACGC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CTGAAAA 773s CTGAAAA 773s Processing line... 773s AGAT 773s AGAT 773s Processing line... 773s AACGC 773s AACGC 773s Processing line... 773s Processing line... 773s AACC 773s AACC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GTTACCTCCTGAAAA 773s GTTACCTCCTGAAAA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GACGA 773s GACGA 773s Processing line... 773s Processing line... 773s AG 773s AG 773s Processing line... 773s CT 773s CT 773s Processing line... 773s AG 773s AG 773s Processing line... 773s AG 773s AG 773s Processing line... 773s CT 773s CT 773s Processing line... 773s AG 773s AG 773s Processing line... 773s CT 773s CT 773s Processing line... 773s Processing line... 773s CATCC 773s CATCC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GAGTGA 773s GAGTGA 773s --- Summary --- 773s Read 1 reference strings 773s Checked 19 alignments, 0 edits 773s --------------- 773s PASSED 773s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 773s /usr/bin/bowtie2 --mp 4.64583185775937,2.56239093272166 --cp-ival 1 --n-ceil 0.0786984093437739,1.29616400561013 -D 32 -a --score-min L,5.35546797756794,5.68414758478876 --rfg 41.6501502437809,3.70691305496153 --rdg 14.492672676629 --gbar 5 -R 3 --ma 24.1063557597996 --cp-min 2 --trim5 1 -q -p 2 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 773s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 773s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 773s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '5' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 773s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '6' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 773s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '9' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 773s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '20' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 773s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '22' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 773s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '28' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 773s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '59' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 773s Warning: skipping read '68' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '68' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 773s 70 reads; of these: 773s 70 (100.00%) were unpaired; of these: 773s 57 (81.43%) aligned 0 times 773s 12 (17.14%) aligned exactly 1 time 773s 1 (1.43%) aligned >1 times 773s 18.57% overall alignment rate 773s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.2 773s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.1 773s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 8 773s Reference gaps introduced: 0 773s Read gaps introduced: 0 773s Rearrangements introduced: 3 773s Created read sampler 773s Sampling 73 reads 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s *** Run 55 of 100 773s /usr/bin/bowtie2 --mm --gbar 7 --score-min L,3.3968808612483,2.66004830603679 --rfg 41.7750572310201 --trim3 1 --cp-ival 1 -k 2 --trim5 7 --cp-min 3 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 773s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '2' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 773s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '10' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 773s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '11' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 773s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '15' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 773s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '16' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 773s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '21' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 773s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '26' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 773s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '27' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 773s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '29' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 773s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '30' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 773s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '33' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 773s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '34' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 773s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '36' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 773s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '37' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 773s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '42' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 773s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '44' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 773s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '46' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 773s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '56' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 773s Read 50 alignments... 773s Read 100 alignments... 773s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 773s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '68' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 773s 73 reads; of these: 773s 63 (86.30%) were paired; of these: 773s 63 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 63 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 63 pairs aligned 0 times concordantly or discordantly; of these: 773s 126 mates make up the pairs; of these: 773s 118 (93.65%) aligned 0 times 773s 5 (3.97%) aligned exactly 1 time 773s 3 (2.38%) aligned >1 times 773s 10 (13.70%) were unpaired; of these: 773s 8 (80.00%) aligned 0 times 773s 2 (20.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 7.35% overall alignment rate 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s /usr/bin/bowtie2 --mm --gbar 7 --score-min L,3.3968808612483,2.66004830603679 --rfg 41.7750572310201 --trim3 1 --cp-ival 1 -k 2 --trim5 7 --cp-min 3 -q -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AACGCAGTTA 773s AACGCAGTTA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s ATATGAGTGATTAATA 773s ATATGAGTGATTAATA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TTA 773s TTA 773s Processing line... 773s TTA 773s TTA 773s Processing line... 773s TCCTGAAAA 773s TCCTGAAAA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TCCTGAAAACATC 773s TCCTGAAAACATC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CGCAG 773s CGCAG 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AT 773s AT 773s Processing line... 773s AT 773s AT 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CCTCCTGA 773s CCTCCTGA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AACA 773s AACA 773s Processing line... 773s AACA 773s AACA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AACGC 773s AACGC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 13 alignments, 0 edits 773s --------------- 773s PASSED 773s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 773s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '2' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 773s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '10' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 773s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '11' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 773s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '15' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 773s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '16' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 773s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '21' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 773s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '26' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 773s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '27' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 773s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '29' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 773s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '30' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 773s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '33' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 773s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '34' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 773s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '36' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 773s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '37' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 773s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '42' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 773s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '44' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 773s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '46' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 773s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '56' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 773s Warning: skipping mate #2 of read '68' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '68' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 773s 73 reads; of these: 773s 63 (86.30%) were paired; of these: 773s 63 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 63 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 63 pairs aligned 0 times concordantly or discordantly; of these: 773s 126 mates make up the pairs; of these: 773s 118 (93.65%) aligned 0 times 773s 5 (3.97%) aligned exactly 1 time 773s 3 (2.38%) aligned >1 times 773s 10 (13.70%) were unpaired; of these: 773s 8 (80.00%) aligned 0 times 773s 2 (20.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 7.35% overall alignment rate 773s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 773s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.2 773s Introducing 0 SNPs, 0/0 ref/read gaps, and 2 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.1 773s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 0 773s Reference gaps introduced: 0 773s Read gaps introduced: 0 773s Rearrangements introduced: 2 773s Created read sampler 773s Sampling 106 reads 773s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 773s *** Run 56 of 100 773s /usr/bin/bowtie2 --mm --score-min L,3.16434428140952,6.78910071033685 --norc --rfg 28.3644012110187,2.23711465120071 --trim3 7 --ma 6.85502648105717 --cp-min 7 --cp-ival 1 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 773s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '7' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 773s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '9' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 773s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '16' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 773s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '18' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 773s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '19' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 773s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '20' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 773s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '32' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 773s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '33' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 773s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '36' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 773s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '38' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 773s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '45' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 773s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '46' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 773s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '48' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 773s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '52' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 773s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '55' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 773s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '60' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 773s Read 50 alignments... 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 773s Warning: skipping mate #1 of read '69' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '69' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 773s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '76' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 773s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '86' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 773s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '88' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 773s Warning: skipping mate #1 of read '89' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '89' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 773s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '94' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 773s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '95' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 773s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '96' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 773s Read 100 alignments... 773s 106 reads; of these: 773s 98 (92.45%) were paired; of these: 773s 93 (94.90%) aligned concordantly 0 times 773s 2 (2.04%) aligned concordantly exactly 1 time 773s 3 (3.06%) aligned concordantly >1 times 773s ---- 773s 93 pairs aligned concordantly 0 times; of these: 773s 1 (1.08%) aligned discordantly 1 time 773s ---- 773s 92 pairs aligned 0 times concordantly or discordantly; of these: 773s 184 mates make up the pairs; of these: 773s 161 (87.50%) aligned 0 times 773s 17 (9.24%) aligned exactly 1 time 773s 6 (3.26%) aligned >1 times 773s 8 (7.55%) were unpaired; of these: 773s 7 (87.50%) aligned 0 times 773s 1 (12.50%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 17.65% overall alignment rate 773s Read 150 alignments... 773s Read 200 alignments... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TAACAACGCAG 773s TAACAACGCAG 773s Processing line... 773s AACGCAGTTACCTCCTGAAAACAT 773s AACGCAGTTACCTCCTGAAAACAT 773s Processing line... 773s CAG 773s CAG 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GTT 773s GTT 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GCAGT 773s GCAGT 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CGCAGTTA 773s CGCAGTTA 773s Processing line... 773s CCTCCTGAAAACATCC 773s CCTCCTGAAAACATCC 773s Processing line... 773s CT 773s CT 773s Processing line... 773s Processing line... 773s CAACGCAGTTACCTCCTGAAA 773s CAACGCAGTTACCTCCTGAAA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AAC 773s AAC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GCAGTTACCTCCTGAAAA 773s GCAGTTACCTCCTGAAAA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AC 773s AC 773s Processing line... 773s ACAAC 773s ACAAC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TGAAAAC 773s TGAAAAC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AACAACGCAGTTACCTCCTGAAAAC 773s AACAACGCAGTTACCTCCTGAAAAC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s ATA 773s ATA 773s Processing line... 773s ATAA 773s ATAA 773s Processing line... 773s CAACGCAGTTACCTCCTGAAAACAT 773s CAACGCAGTTACCTCCTGAAAACAT 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AG 773s AG 773s Processing line... 773s Processing line... 773s Processing line... 773s CT 773s CT 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CAGTT 773s CAGTT 773s Processing line... 773s Processing line... 773s GATATGA 773s GATATGA 773s Processing line... 773s GAGATATGAGTGATT 773s GAGATATGAGTGATT 773s Processing line... 773s Processing line... 773s Processing line... 773s AGTTAC 773s AGTTAC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CAGTTACCTCC 773s CAGTTACCTCC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GTC 773s GTC 773s Processing line... 773s Processing line... 773s AAC 773s AAC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s ACGCAGTTAC 773s ACGCAGTTAC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TCCTGAAAACA 773s TCCTGAAAACA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CCTCCTGAAAACATC 773s CCTCCTGAAAACATC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s ACAACGCAGTTACCTCCTGAAAA 773s ACAACGCAGTTACCTCCTGAAAA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GAA 773s GAA 773s Processing line... 773s ATA 773s ATA 773s Processing line... 773s GAAAAC 773s GAAAAC 773s Processing line... 773s TC 773s TC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CTGAA 773s CTGAA 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 36 alignments, 0 edits 773s --------------- 773s PASSED 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.1 773s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.2 773s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 0 773s Reference gaps introduced: 0 773s Read gaps introduced: 0 773s Rearrangements introduced: 0 773s Created read sampler 773s Sampling 109 reads 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s *** Run 57 of 100 773s /usr/bin/bowtie2 --trim5 9 --np 4 --cp-min 3 -a --score-min L,4.18160846384089,6.76996401997606 --rdg 12.722814040463,2.77111736151622 --rfg 44.9944558686245 --trim3 5 --cp-ival 1 --local --nofw --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 773s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 773s Warning: skipping mate #2 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 773s Read 50 alignments... 773s Read 100 alignments... 773s Warning: skipping mate #1 of read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 773s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 773s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 773s 109 reads; of these: 773s 76 (69.72%) were paired; of these: 773s 76 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 76 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 76 pairs aligned 0 times concordantly or discordantly; of these: 773s 152 mates make up the pairs; of these: 773s 152 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 33 (30.28%) were unpaired; of these: 773s 33 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s Read 150 alignments... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing 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line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 0 alignments, 0 edits 773s --------------- 773s PASSED 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.1 773s Introducing 6 SNPs, 2/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.2 773s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 11 773s Reference gaps introduced: 2 773s Read gaps introduced: 0 773s Rearrangements introduced: 0 773s Created read sampler 773s Sampling 145 reads 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s *** Run 58 of 100 773s /usr/bin/bowtie2 --cp-min 5 --local --cp-ival 4 --mp 4.03684232436661,1.16213486007483 --score-min L,8.96709487131008,3.54726047465445 --rdg 24.8945819526163 -a -i C,0.68052603297155 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '8' because it was < 2 characters long 773s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '28' because it was < 2 characters long 773s Read 50 alignments... 773s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '89' because it was < 2 characters long 773s Warning: skipping mate #1 of read '120' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '120' because it was < 2 characters long 773s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '123' because it was < 2 characters long 773s Warning: skipping mate #1 of read '132' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '132' because it was < 2 characters long 773s Warning: skipping mate #1 of read '144' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '144' because it was < 2 characters long 773s Read 100 alignments... 773s Read 150 alignments... 773s Read 200 alignments... 773s 145 reads; of these: 773s 145 (100.00%) were paired; of these: 773s 145 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 145 pairs aligned concordantly 0 times; of these: 773s 0 (0.00%) aligned discordantly 1 time 773s ---- 773s 145 pairs aligned 0 times concordantly or discordantly; of these: 773s 290 mates make up the pairs; of these: 773s 290 (100.00%) aligned 0 times 773s 0 (0.00%) aligned exactly 1 time 773s 0 (0.00%) aligned >1 times 773s 0.00% overall alignment rate 773s Read 250 alignments... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s 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Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 0 alignments, 0 edits 773s --------------- 773s PASSED 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.1 773s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.2 773s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 0 773s Reference gaps introduced: 0 773s Read gaps introduced: 1 773s Rearrangements introduced: 0 773s Created read sampler 773s Sampling 72 reads 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s *** Run 59 of 100 773s /usr/bin/bowtie2 --np 6 --trim5 4 --cp-min 2 --rdg 13.0231259646666 --score-min L,4.71253395619122,3.92898967301665 -a --mm --cp-ival 4 -N 0 -L31 --trim3 9 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 773s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '2' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 773s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '3' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 773s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '6' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 773s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '7' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 773s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '12' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 773s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '28' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 773s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '30' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 773s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 773s Warning: skipping mate #2 of read '31' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 773s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '32' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 773s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '35' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 773s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '38' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 773s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '42' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 773s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '43' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 773s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '52' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 773s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '60' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 773s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 773s Warning: skipping mate #1 of read '61' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 773s Read 50 alignments... 773s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 773s Read 100 alignments... 773s 72 reads; of these: 773s 53 (73.61%) were paired; of these: 773s 53 (100.00%) aligned concordantly 0 times 773s 0 (0.00%) aligned concordantly exactly 1 time 773s 0 (0.00%) aligned concordantly >1 times 773s ---- 773s 53 pairs aligned concordantly 0 times; of these: 773s 2 (3.77%) aligned discordantly 1 time 773s ---- 773s 51 pairs aligned 0 times concordantly or discordantly; of these: 773s 102 mates make up the pairs; of these: 773s 87 (85.29%) aligned 0 times 773s 13 (12.75%) aligned exactly 1 time 773s 2 (1.96%) aligned >1 times 773s 19 (26.39%) were unpaired; of these: 773s 15 (78.95%) aligned 0 times 773s 3 (15.79%) aligned exactly 1 time 773s 1 (5.26%) aligned >1 times 773s 18.40% overall alignment rate 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TAACAACGCAGTTACCTCCTGA 773s TAACAACGCAGTTACCTCCTGA 773s Processing line... 773s Processing line... 773s AGTTACCTCCTGAAAACA 773s AGTTACCTCCTGAAAACA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AAC 773s AAC 773s Processing line... 773s AAC 773s AAC 773s Processing line... 773s GTT 773s GTT 773s Processing line... 773s AAC 773s AAC 773s Processing line... 773s AAC 773s AAC 773s Processing line... 773s AAC 773s AAC 773s Processing line... 773s Processing line... 773s Processing line... 773s CGAC 773s CGAC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CGCAGTTACCTCC 773s CGCAGTTACCTCC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s ATAGA 773s ATAGA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TAACAA 773s TAACAA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CGCAGTT 773s CGCAGTT 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TTACCTC 773s TTACCTC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s ACCTCCTGA 773s ACCTCCTGA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s TCC 773s TCC 773s Processing line... 773s TCC 773s TCC 773s Processing line... 773s Processing line... 773s TAACAACGCAGTTACCTCCTG 773s TAACAACGCAGTTACCTCCTG 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CAACGCAGTTACCTCCTGAAAAC 773s CAACGCAGTTACCTCCTGAAAAC 773s Processing line... 773s Processing line... 773s GACGA 773s GACGA 773s Processing line... 773s ATAG 773s ATAG 773s Processing line... 773s CG 773s CG 773s Processing line... 773s CG 773s CG 773s Processing line... 773s CG 773s CG 773s Processing line... 773s CG 773s CG 773s Processing line... 773s CG 773s CG 773s Processing line... 773s CG 773s CG 773s Processing line... 773s CG 773s CG 773s Processing line... 773s CG 773s CG 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s GCAGTTACCTCCTGAAAACATC 773s GCAGTTACCTCCTGAAAACATC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CGCAGT 773s CGCAGT 773s Processing line... 773s CTCCTGAAAA 773s CTCCTGAAAA 773s Processing line... 773s GCAGTTACCTCCT 773s GCAGTTACCTCCT 773s Processing line... 773s Processing line... 773s Processing line... 773s ACGCAGTTACCT 773s ACGCAGTTACCT 773s Processing line... 773s Processing line... 773s ACGA 773s ACGA 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CTCCTGA 773s CTCCTGA 773s Processing line... 773s Processing line... 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 36 alignments, 0 edits 773s --------------- 773s PASSED 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.1 773s Introducing 3 SNPs, 1/0 ref/read gaps, and 3 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.2 773s Introducing 9 SNPs, 1/1 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 12 773s Reference gaps introduced: 2 773s Read gaps introduced: 1 773s Rearrangements introduced: 3 773s Created read sampler 773s Sampling 103 reads 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s *** Run 60 of 100 773s /usr/bin/bowtie2 --ma 12.4816857925352 --cp-min 2 -k 2 --mp 7.18608503593934,3.64787008011199 --nofw --cp-ival 3 --trim3 7 --score-min L,7.54639816910208,8.26177502947435 --gbar 8 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 773s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 773s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 773s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '14' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 773s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '17' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 773s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '22' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 773s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '24' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 773s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '26' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 773s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '29' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 773s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '30' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 773s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '32' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 773s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '39' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 773s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '43' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 773s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '47' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 773s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '49' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 773s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '52' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 773s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '57' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 773s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '59' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 773s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '63' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 773s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '64' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 773s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '66' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 773s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '69' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 773s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '76' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 773s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '85' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 773s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '86' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 773s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '88' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 773s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '93' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 773s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '96' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 773s 103 reads; of these: 773s 103 (100.00%) were unpaired; of these: 773s 99 (96.12%) aligned 0 times 773s 2 (1.94%) aligned exactly 1 time 773s 2 (1.94%) aligned >1 times 773s 3.88% overall alignment rate 773s Read 50 alignments... 773s Read 100 alignments... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CGTC 773s CGTC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s CT 773s CT 773s Processing line... 773s CT 773s CT 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AGTTACC 773s AGTTACC 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s AG 773s AG 773s Processing line... 773s AG 773s AG 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s Processing line... 773s --- Summary --- 773s Read 1 reference strings 773s Checked 6 alignments, 0 edits 773s --------------- 773s PASSED 773s ALSO checking that bowtie2 and bowtie2-align match up 773s /usr/bin/bowtie2 --ma 12.4816857925352 --cp-min 2 -k 2 --mp 7.18608503593934,3.64787008011199 --nofw --cp-ival 3 --trim3 7 --score-min L,7.54639816910208,8.26177502947435 --gbar 8 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 773s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 773s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 773s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '14' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 773s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '17' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 773s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '22' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 773s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '24' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 773s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '26' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 773s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '29' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 773s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '30' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 773s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '32' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 773s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '39' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 773s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '43' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 773s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '47' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 773s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '49' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 773s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '52' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 773s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '57' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 773s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '59' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 773s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '63' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 773s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '64' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 773s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '66' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 773s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '69' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 773s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '76' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 773s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '85' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 773s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '86' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 773s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '88' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 773s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 773s Warning: skipping read '93' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 773s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 773s Warning: skipping read '96' because it was < 2 characters long 773s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 773s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 773s 103 reads; of these: 773s 103 (100.00%) were unpaired; of these: 773s 99 (96.12%) aligned 0 times 773s 2 (1.94%) aligned exactly 1 time 773s 2 (1.94%) aligned >1 times 773s 3.88% overall alignment rate 773s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 773s Flattened IUPAC characters 773s Mutating sequence Sim.pm.1 773s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutating sequence Sim.pm.2 773s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 773s Finished SNPs 773s Finished ref gaps 773s Finished read gaps 773s Mutated reference genome to subject genome 773s SNPs introduced: 2 773s Reference gaps introduced: 0 773s Read gaps introduced: 1 773s Rearrangements introduced: 0 773s Created read sampler 773s Sampling 57 reads 773s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 773s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 773s parsing sequence Sim.pm.1... 773s parsing sequence Sim.pm.2... 773s Parsed 74 reference bases 773s *** Run 61 of 100 773s /usr/bin/bowtie2 --cp-min 2 --np 4 --mp 8.37296534222646,1.60591235221482 -N 0 -L19 --cp-ival 1 --n-ceil 1.47458602038203,1.20086522729767 --trim3 4 --rfg 1.55737177067278 --score-min L,4.36830551983135,7.42611852438193 --gbar 4 -a --mm -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 774s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '5' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 774s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '7' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 774s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '15' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 774s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '16' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 774s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '17' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 774s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '20' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 774s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '28' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 774s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '30' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 774s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '39' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 774s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '41' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 774s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '42' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 774s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '44' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 774s 57 reads; of these: 774s 51 (89.47%) were paired; of these: 774s 50 (98.04%) aligned concordantly 0 times 774s 1 (1.96%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 50 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 50 pairs aligned 0 times concordantly or discordantly; of these: 774s 100 mates make up the pairs; of these: 774s 89 (89.00%) aligned 0 times 774s 7 (7.00%) aligned exactly 1 time 774s 4 (4.00%) aligned >1 times 774s 6 (10.53%) were unpaired; of these: 774s 5 (83.33%) aligned 0 times 774s 1 (16.67%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 12.96% overall alignment rate 774s Read 50 alignments... 774s Read 100 alignments... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CAAC 774s CAAC 774s Processing line... 774s Processing line... 774s ACCTCCTGAAAACA 774s ACCTCCTGAAAACA 774s Processing line... 774s CCTCCTGAAAACAT 774s CCTCCTGAAAACAT 774s Processing line... 774s Processing line... 774s Processing line... 774s ATAGAC 774s ATAGAC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s TG 774s TG 774s Processing line... 774s CA 774s CA 774s Processing line... 774s TG 774s TG 774s Processing line... 774s TG 774s TG 774s Processing line... 774s CA 774s CA 774s Processing line... 774s CA 774s CA 774s Processing line... 774s TG 774s TG 774s Processing line... 774s CA 774s CA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CCTGAA 774s CCTGAA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CTCCT 774s CTCCT 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AAAACATC 774s AAAACATC 774s Processing line... 774s Processing line... 774s Processing line... 774s TTACCTCCTG 774s TTACCTCCTG 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s TAACAACGCAGTTACCT 774s TAACAACGCAGTTACCT 774s Processing line... 774s Processing line... 774s CT 774s CT 774s Processing line... 774s CT 774s CT 774s Processing line... 774s CT 774s CT 774s Processing line... 774s AG 774s AG 774s Processing line... 774s AG 774s AG 774s Processing line... 774s AG 774s AG 774s Processing line... 774s AG 774s AG 774s Processing line... 774s Processing line... 774s AG 774s AG 774s Processing line... 774s AG 774s AG 774s Processing line... 774s CT 774s CT 774s Processing line... 774s CT 774s CT 774s Processing line... 774s AG 774s AG 774s Processing line... 774s AG 774s AG 774s Processing line... 774s CT 774s CT 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AAA 774s AAA 774s Processing line... 774s AAA 774s AAA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AACGCAGTTACCTCCTGAAAA 774s AACGCAGTTACCTCCTGAAAA 774s Processing line... 774s --- Summary --- 774s Read 1 reference strings 774s Checked 34 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2-align match up 774s /usr/bin/bowtie2 --cp-min 2 --np 4 --mp 8.37296534222646,1.60591235221482 -N 0 -L19 --cp-ival 1 --n-ceil 1.47458602038203,1.20086522729767 --trim3 4 --rfg 1.55737177067278 --score-min L,4.36830551983135,7.42611852438193 --gbar 4 -a --mm -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 774s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '5' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 774s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '7' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 774s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '15' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 774s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '16' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 774s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '17' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 774s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '20' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 774s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '28' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 774s Warning: skipping mate #2 of read '30' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '30' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 774s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '39' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 774s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '41' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 774s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '42' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 774s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '44' because it was < 2 characters long 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 774s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 774s 57 reads; of these: 774s 51 (89.47%) were paired; of these: 774s 50 (98.04%) aligned concordantly 0 times 774s 1 (1.96%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 50 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 50 pairs aligned 0 times concordantly or discordantly; of these: 774s 100 mates make up the pairs; of these: 774s 89 (89.00%) aligned 0 times 774s 7 (7.00%) aligned exactly 1 time 774s 4 (4.00%) aligned >1 times 774s 6 (10.53%) were unpaired; of these: 774s 5 (83.33%) aligned 0 times 774s 1 (16.67%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 12.96% overall alignment rate 774s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.1 774s *** Run 62 of 100 774s /usr/bin/bowtie2 --cp-min 6 --norc --trim5 8 --cp-ival 2 --local -N 0 --rfg 20.9113307862836 --score-min L,9.14239760120576,7.42849294162444 --mm -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 774s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.2 774s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 9 774s Reference gaps introduced: 0 774s Read gaps introduced: 0 774s Rearrangements introduced: 0 774s Created read sampler 774s Sampling 110 reads 774s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 774s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s Parsed 74 reference bases 774s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '1' because it was < 2 characters long 774s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '3' because it was < 2 characters long 774s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '8' because it was < 2 characters long 774s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '9' because it was < 2 characters long 774s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '10' because it was < 2 characters long 774s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '16' because it was < 2 characters long 774s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '18' because it was < 2 characters long 774s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '21' because it was < 2 characters long 774s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '22' because it was < 2 characters long 774s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '23' because it was < 2 characters long 774s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '24' because it was < 2 characters long 774s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '25' because it was < 2 characters long 774s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '26' because it was < 2 characters long 774s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '28' because it was < 2 characters long 774s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '29' because it was < 2 characters long 774s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '31' because it was < 2 characters long 774s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '32' because it was < 2 characters long 774s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '33' because it was < 2 characters long 774s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '34' because it was < 2 characters long 774s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '35' because it was < 2 characters long 774s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '37' because it was < 2 characters long 774s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '42' because it was < 2 characters long 774s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '45' because it was < 2 characters long 774s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '48' because it was < 2 characters long 774s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '50' because it was < 2 characters long 774s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '56' because it was < 2 characters long 774s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '58' because it was < 2 characters long 774s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '61' because it was < 2 characters long 774s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '68' because it was < 2 characters long 774s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '69' because it was < 2 characters long 774s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '70' because it was < 2 characters long 774s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '73' because it was < 2 characters long 774s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '81' because it was < 2 characters long 774s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '83' because it was < 2 characters long 774s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '86' because it was < 2 characters long 774s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '87' because it was < 2 characters long 774s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '89' because it was < 2 characters long 774s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '93' because it was < 2 characters long 774s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '99' because it was < 2 characters long 774s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '110' because it was < 2 characters long 774s 110 reads; of these: 774s 110 (100.00%) were unpaired; of these: 774s 110 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s Read 50 alignments... 774s Read 100 alignments... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s --- Summary --- 774s Read 1 reference strings 774s Checked 0 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2-align match up 774s /usr/bin/bowtie2 --cp-min 6 --norc --trim5 8 --cp-ival 2 --local -N 0 --rfg 20.9113307862836 --score-min L,9.14239760120576,7.42849294162444 --mm -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 774s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '1' because it was < 2 characters long 774s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '3' because it was < 2 characters long 774s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '8' because it was < 2 characters long 774s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '9' because it was < 2 characters long 774s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '10' because it was < 2 characters long 774s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '16' because it was < 2 characters long 774s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '18' because it was < 2 characters long 774s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '21' because it was < 2 characters long 774s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '22' because it was < 2 characters long 774s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '23' because it was < 2 characters long 774s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '24' because it was < 2 characters long 774s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '25' because it was < 2 characters long 774s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '26' because it was < 2 characters long 774s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '28' because it was < 2 characters long 774s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '29' because it was < 2 characters long 774s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '31' because it was < 2 characters long 774s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '32' because it was < 2 characters long 774s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '33' because it was < 2 characters long 774s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '34' because it was < 2 characters long 774s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '35' because it was < 2 characters long 774s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '37' because it was < 2 characters long 774s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '42' because it was < 2 characters long 774s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '45' because it was < 2 characters long 774s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '48' because it was < 2 characters long 774s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '50' because it was < 2 characters long 774s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '56' because it was < 2 characters long 774s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '58' because it was < 2 characters long 774s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '61' because it was < 2 characters long 774s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '68' because it was < 2 characters long 774s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '69' because it was < 2 characters long 774s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '70' because it was < 2 characters long 774s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '73' because it was < 2 characters long 774s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '81' because it was < 2 characters long 774s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '83' because it was < 2 characters long 774s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '86' because it was < 2 characters long 774s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '87' because it was < 2 characters long 774s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '89' because it was < 2 characters long 774s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '93' because it was < 2 characters long 774s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '99' because it was < 2 characters long 774s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '110' because it was < 2 characters long 774s 110 reads; of these: 774s 110 (100.00%) were unpaired; of these: 774s 110 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 774s /usr/bin/bowtie2 --cp-min 6 --norc --trim5 8 --cp-ival 2 --local -N 0 --rfg 20.9113307862836 --score-min L,9.14239760120576,7.42849294162444 --mm -q -p 2 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 774s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 774s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '1' because it was < 2 characters long 774s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '3' because it was < 2 characters long 774s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '8' because it was < 2 characters long 774s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '9' because it was < 2 characters long 774s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '10' because it was < 2 characters long 774s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '16' because it was < 2 characters long 774s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '18' because it was < 2 characters long 774s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '21' because it was < 2 characters long 774s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '22' because it was < 2 characters long 774s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '23' because it was < 2 characters long 774s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '24' because it was < 2 characters long 774s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '25' because it was < 2 characters long 774s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '26' because it was < 2 characters long 774s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '28' because it was < 2 characters long 774s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '29' because it was < 2 characters long 774s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '31' because it was < 2 characters long 774s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '32' because it was < 2 characters long 774s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '33' because it was < 2 characters long 774s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '34' because it was < 2 characters long 774s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '35' because it was < 2 characters long 774s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '37' because it was < 2 characters long 774s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '42' because it was < 2 characters long 774s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '45' because it was < 2 characters long 774s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '48' because it was < 2 characters long 774s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '50' because it was < 2 characters long 774s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '56' because it was < 2 characters long 774s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '58' because it was < 2 characters long 774s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '61' because it was < 2 characters long 774s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '68' because it was < 2 characters long 774s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '69' because it was < 2 characters long 774s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '70' because it was < 2 characters long 774s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '73' because it was < 2 characters long 774s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '81' because it was < 2 characters long 774s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '83' because it was < 2 characters long 774s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '86' because it was < 2 characters long 774s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '87' because it was < 2 characters long 774s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '89' because it was < 2 characters long 774s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '93' because it was < 2 characters long 774s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '99' because it was < 2 characters long 774s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 774s Warning: skipping read '110' because it was < 2 characters long 774s 110 reads; of these: 774s 110 (100.00%) were unpaired; of these: 774s 110 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.1 774s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.2 774s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 10 774s Reference gaps introduced: 0 774s Read gaps introduced: 0 774s Rearrangements introduced: 1 774s Created read sampler 774s Sampling 85 reads 774s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 774s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s Parsed 74 reference bases 774s *** Run 63 of 100 774s /usr/bin/bowtie2 --cp-min 2 --np 3 --cp-ival 1 -D 41 --local --trim3 7 --score-min L,7.60788820296084,3.86829550927743 --rdg 49.0200750067394 -a --mm -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 774s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '1' because it was < 2 characters long 774s Warning: skipping mate #1 of read '4' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '4' because it was < 2 characters long 774s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '9' because it was < 2 characters long 774s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '12' because it was < 2 characters long 774s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '14' because it was < 2 characters long 774s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '18' because it was < 2 characters long 774s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '24' because it was < 2 characters long 774s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '25' because it was < 2 characters long 774s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '32' because it was < 2 characters long 774s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '45' because it was < 2 characters long 774s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '47' because it was < 2 characters long 774s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '49' because it was < 2 characters long 774s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '62' because it was < 2 characters long 774s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '70' because it was < 2 characters long 774s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '76' because it was < 2 characters long 774s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '77' because it was < 2 characters long 774s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '78' because it was < 2 characters long 774s Read 50 alignments... 774s 85 reads; of these: 774s 72 (84.71%) were paired; of these: 774s 72 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 72 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 72 pairs aligned 0 times concordantly or discordantly; of these: 774s 144 mates make up the pairs; of these: 774s 144 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 13 (15.29%) were unpaired; of these: 774s 13 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s Read 100 alignments... 774s Read 150 alignments... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s --- Summary --- 774s Read 1 reference strings 774s Checked 0 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 774s /usr/bin/bowtie2 --cp-min 2 --np 3 --cp-ival 1 -D 41 --local --trim3 7 --score-min L,7.60788820296084,3.86829550927743 --rdg 49.0200750067394 -a --mm -q -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 774s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '1' because it was < 2 characters long 774s Warning: skipping mate #1 of read '4' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '4' because it was < 2 characters long 774s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '9' because it was < 2 characters long 774s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '12' because it was < 2 characters long 774s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '14' because it was < 2 characters long 774s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '18' because it was < 2 characters long 774s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '24' because it was < 2 characters long 774s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '25' because it was < 2 characters long 774s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '32' because it was < 2 characters long 774s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '45' because it was < 2 characters long 774s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '47' because it was < 2 characters long 774s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '49' because it was < 2 characters long 774s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '62' because it was < 2 characters long 774s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '70' because it was < 2 characters long 774s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '76' because it was < 2 characters long 774s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '77' because it was < 2 characters long 774s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '78' because it was < 2 characters long 774s 85 reads; of these: 774s 72 (84.71%) were paired; of these: 774s 72 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 72 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 72 pairs aligned 0 times concordantly or discordantly; of these: 774s 144 mates make up the pairs; of these: 774s 144 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 13 (15.29%) were unpaired; of these: 774s 13 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.1 774s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.2 774s Introducing 8 SNPs, 2/2 ref/read gaps, and 1 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 10 774s Reference gaps introduced: 2 774s Read gaps introduced: 2 774s Rearrangements introduced: 1 774s Created read sampler 774s Sampling 78 reads 774s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 774s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s Parsed 74 reference bases 774s *** Run 64 of 100 774s /usr/bin/bowtie2 --trim3 7 -N 1 -L22 --nofw --cp-ival 1 --local --rdg 39.654995983315 --score-min L,1.48528003890477,8.85818939420679 --gbar 3 --cp-min 5 -k 3 --norc --np 3 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 774s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 774s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (1) 774s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 774s Read 50 alignments... 774s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 774s Read 100 alignments... 774s 78 reads; of these: 774s 68 (87.18%) were paired; of these: 774s 68 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 68 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 68 pairs aligned 0 times concordantly or discordantly; of these: 774s 136 mates make up the pairs; of these: 774s 136 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 10 (12.82%) were unpaired; of these: 774s 10 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s Read 150 alignments... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s --- Summary --- 774s Read 1 reference strings 774s Checked 0 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2-align match up 774s /usr/bin/bowtie2 --trim3 7 -N 1 -L22 --nofw --cp-ival 1 --local --rdg 39.654995983315 --score-min L,1.48528003890477,8.85818939420679 --gbar 3 --cp-min 5 -k 3 --norc --np 3 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 774s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 774s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (1) 774s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 774s 78 reads; of these: 774s 68 (87.18%) were paired; of these: 774s 68 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 68 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 68 pairs aligned 0 times concordantly or discordantly; of these: 774s 136 mates make up the pairs; of these: 774s 136 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 10 (12.82%) were unpaired; of these: 774s 10 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 774s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 774s /usr/bin/bowtie2 --trim3 7 -N 1 -L22 --nofw --cp-ival 1 --local --rdg 39.654995983315 --score-min L,1.48528003890477,8.85818939420679 --gbar 3 --cp-min 5 -k 3 --norc --np 3 --qseq -p 4 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 774s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 774s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (1) 774s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 774s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 774s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 774s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 774s 78 reads; of these: 774s 68 (87.18%) were paired; of these: 774s 68 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 68 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 68 pairs aligned 0 times concordantly or discordantly; of these: 774s 136 mates make up the pairs; of these: 774s 136 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 10 (12.82%) were unpaired; of these: 774s 10 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.1 774s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.2 774s Introducing 3 SNPs, 0/2 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 4 774s Reference gaps introduced: 0 774s Read gaps introduced: 2 774s Rearrangements introduced: 0 774s Created read sampler 774s Sampling 133 reads 774s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 774s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s Parsed 74 reference bases 774s *** Run 65 of 100 774s /usr/bin/bowtie2 -M 3 --cp-min 5 --rdg 48.5044444365789,16.7248976866791 --rfg 48.5649836869089,7.27266390629878 --score-min L,8.00116825946574,1.10565526829134 --cp-ival 1 --local -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 774s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 774s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '21' because it was < 2 characters long 774s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '40' because it was < 2 characters long 774s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '64' because it was < 2 characters long 774s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '65' because it was < 2 characters long 774s Read 50 alignments... 774s Read 100 alignments... 774s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '76' because it was < 2 characters long 774s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '77' because it was < 2 characters long 774s Warning: skipping mate #2 of read '77' because it was < 2 characters long 774s Read 150 alignments... 774s Warning: skipping mate #2 of read '131' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '131' because it was < 2 characters long 774s Read 200 alignments... 774s 133 reads; of these: 774s 133 (100.00%) were paired; of these: 774s 133 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 133 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 133 pairs aligned 0 times concordantly or discordantly; of these: 774s 266 mates make up the pairs; of these: 774s 242 (90.98%) aligned 0 times 774s 24 (9.02%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 9.02% overall alignment rate 774s Read 250 alignments... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s TGAAAACATC 774s TGAAAACATC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s ACGTAACAACGCAGTTACCTCCTGAAA 774s ACNTAACAACGCAGTTACCTCCTGAAA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AACAACGCAGTTACCTCGTGAAAAC 774s AACAACGCAGTTACCTCCTGAAAAC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s /usr/bin/bowtie2 -M 3 --cp-min 5 --rdg 48.5044444365789,16.7248976866791 --rfg 48.5649836869089,7.27266390629878 --score-min L,8.00116825946574,1.10565526829134 --cp-ival 1 --local -q -p 4 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s TTACCTCCTGAAAACA 774s TTACCTCCTGAAAACA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CTGAAAACATCC 774s CTGAAAACATCC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CGACGTAACAACGCAGTTACCTCCTGAA 774s CGACNTAACAACGCAGTTACCTCCTGAA 774s Processing line... 774s Processing line... 774s CGAGATATGAGTG 774s CGAGATATGAGTG 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s TAGACGAC 774s TAGACGAC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CAACGCAGTTACCTCGTGAAAACA 774s CAACGCAGTTACCTCCTGAAAACA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CAACGCAGTTACCTCCTGAAA 774s CAACGCAGTTACCTCCTGAAA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s GCAGTTACCTCGTGAAAACAT 774s GCAGTTACCTCCTGAAAACAT 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s ACAACGCAGTTACCTCGTGAAAACAT 774s ACAACGCAGTTACCTCCTGAAAACAT 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s TAACAACGCAGTTACC 774s TAACAACGCAGTTACC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AACAACGCAGTTACCTCGTGAAAACATCC 774s AACAACGCAGTTACCTCCTGAAAACATCC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AACGCAGTTACCTCGTGAAAAC 774s AACGCAGTTACCTCCTGAAAAC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s CTCCTGAA 774s CTCCTGAA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s ACAACGCAGTTAC 774s ACAACGCAGTTAC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s ACCTCCTGAA 774s ACCTCCTGAA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AACAACGCAGTT 774s AACAACGCAGTT 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s ATAGACGACGTAACAACGCAGTTACCTCCTGAAAACA 774s ATAGACGACNTAACAACGCAGTTACCTCCTGAAAACA 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s ACGCAGTTACCTCC 774s ACGCAGTTACCTCC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s TACCTCCT 774s TACCTCCT 774s Processing line... 774s Processing line... 774s ATAGACGACGTAACAACGCAGTTACCTCCTGAAAACATC 774s ATAGACGACNTAACAACGCAGTTACCTCCTGAAAACATC 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s AGTTACCTCCTGAAAACATCC 774s AGTTACCTCCTGAAAACATCC 774s Processing line... 774s Processing line... 774s Processing line... 774s --- Summary --- 774s Read 1 reference strings 774s Checked 24 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 774s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 774s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '21' because it was < 2 characters long 774s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '40' because it was < 2 characters long 774s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '64' because it was < 2 characters long 774s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '65' because it was < 2 characters long 774s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '76' because it was < 2 characters long 774s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '77' because it was < 2 characters long 774s Warning: skipping mate #2 of read '77' because it was < 2 characters long 774s Warning: skipping mate #2 of read '131' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '131' because it was < 2 characters long 774s 133 reads; of these: 774s 133 (100.00%) were paired; of these: 774s 133 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 133 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 133 pairs aligned 0 times concordantly or discordantly; of these: 774s 266 mates make up the pairs; of these: 774s 242 (90.98%) aligned 0 times 774s 24 (9.02%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 9.02% overall alignment rate 774s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 774s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 774s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 774s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 774s /usr/bin/bowtie2 -M 3 --cp-min 5 --rdg 48.5044444365789,16.7248976866791 --rfg 48.5649836869089,7.27266390629878 --score-min L,8.00116825946574,1.10565526829134 --cp-ival 1 --local -q -p 2 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 774s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 774s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '21' because it was < 2 characters long 774s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '40' because it was < 2 characters long 774s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '64' because it was < 2 characters long 774s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '65' because it was < 2 characters long 774s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '76' because it was < 2 characters long 774s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #1 of read '77' because it was < 2 characters long 774s Warning: skipping mate #2 of read '77' because it was < 2 characters long 774s Warning: skipping mate #2 of read '131' because length (1) <= # seed mismatches (0) 774s Warning: skipping mate #2 of read '131' because it was < 2 characters long 774s 133 reads; of these: 774s 133 (100.00%) were paired; of these: 774s 133 (100.00%) aligned concordantly 0 times 774s 0 (0.00%) aligned concordantly exactly 1 time 774s 0 (0.00%) aligned concordantly >1 times 774s ---- 774s 133 pairs aligned concordantly 0 times; of these: 774s 0 (0.00%) aligned discordantly 1 time 774s ---- 774s 133 pairs aligned 0 times concordantly or discordantly; of these: 774s 266 mates make up the pairs; of these: 774s 242 (90.98%) aligned 0 times 774s 24 (9.02%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 9.02% overall alignment rate 774s Flattened IUPAC characters 774s Mutating sequence Sim.pm.2 774s Introducing 6 SNPs, 2/0 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutating sequence Sim.pm.1 774s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 774s Finished SNPs 774s Finished ref gaps 774s Finished read gaps 774s Mutated reference genome to subject genome 774s SNPs introduced: 9 774s Reference gaps introduced: 2 774s Read gaps introduced: 0 774s Rearrangements introduced: 0 774s Created read sampler 774s Sampling 32 reads 774s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 774s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 774s parsing sequence Sim.pm.1... 774s parsing sequence Sim.pm.2... 774s Parsed 74 reference bases 774s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 774s *** Run 66 of 100 774s /usr/bin/bowtie2 -R 3 --cp-min 6 --n-ceil 0.428064310637054,0.939926231463314 -D 49 --local --cp-ival 2 --score-min L,4.36659859128337,3.65181355616271 --rfg 17.4376761732635 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 774s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 774s Warning: skipping read '8' because it was < 2 characters long 774s 32 reads; of these: 774s 32 (100.00%) were unpaired; of these: 774s 32 (100.00%) aligned 0 times 774s 0 (0.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 0.00% overall alignment rate 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s Processing line... 774s --- Summary --- 774s Read 1 reference strings 774s Checked 0 alignments, 0 edits 774s --------------- 774s PASSED 774s ALSO checking that bowtie2 and bowtie2-align match up 774s /usr/bin/bowtie2 -R 3 --cp-min 6 --n-ceil 0.428064310637054,0.939926231463314 -D 49 --local --cp-ival 2 --score-min L,4.36659859128337,3.65181355616271 --rfg 17.4376761732635 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 775s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '8' because it was < 2 characters long 775s 32 reads; of these: 775s 32 (100.00%) were unpaired; of these: 775s 32 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 775s /usr/bin/bowtie2 -R 3 --cp-min 6 --n-ceil 0.428064310637054,0.939926231463314 -D 49 --local --cp-ival 2 --score-min L,4.36659859128337,3.65181355616271 --rfg 17.4376761732635 -f -p 2 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 775s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 775s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '8' because it was < 2 characters long 775s 32 reads; of these: 775s 32 (100.00%) were unpaired; of these: 775s 32 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 775s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.2 775s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.1 775s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 0 775s Reference gaps introduced: 0 775s Read gaps introduced: 1 775s Rearrangements introduced: 0 775s Created read sampler 775s Sampling 10 reads 775s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 775s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 74 reference bases 775s *** Run 67 of 100 775s /usr/bin/bowtie2 --ma 16.4496145910664 --cp-min 6 -a --mm --score-min L,8.98707501166564,8.41885638963561 --rfg 9.12761271365317,6.42979014270574 --trim3 7 --mp 7.94144335390194,1.58677554031644 --cp-ival 1 --n-ceil 0.513834862353263,0.437559071785082 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 775s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 775s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 775s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '4' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 775s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '5' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 775s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '7' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 775s 10 reads; of these: 775s 10 (100.00%) were unpaired; of these: 775s 10 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 0 alignments, 0 edits 775s --------------- 775s PASSED 775s ALSO checking that bowtie2 and bowtie2-align match up 775s /usr/bin/bowtie2 --ma 16.4496145910664 --cp-min 6 -a --mm --score-min L,8.98707501166564,8.41885638963561 --rfg 9.12761271365317,6.42979014270574 --trim3 7 --mp 7.94144335390194,1.58677554031644 --cp-ival 1 --n-ceil 0.513834862353263,0.437559071785082 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 775s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 775s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 775s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '4' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 775s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '5' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 775s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '7' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 775s 10 reads; of these: 775s 10 (100.00%) were unpaired; of these: 775s 10 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.1 775s Introducing 3 SNPs, 2/0 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.2 775s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 5 775s Reference gaps introduced: 3 775s Read gaps introduced: 0 775s Rearrangements introduced: 1 775s Created read sampler 775s Sampling 85 reads 775s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 775s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 74 reference bases 775s *** Run 68 of 100 775s /usr/bin/bowtie2 --trim5 1 --np 1 --cp-min 4 --mm -a --rfg 40.6440204888311,15.7934757161166 --rdg 17.5036866263549 --score-min L,3.67550346414456,7.69255860469653 --mp 5.53822942811507,2.40938356742151 --local --cp-ival 1 -D 24 -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw 775s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '9' because it was < 2 characters long 775s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '10' because it was < 2 characters long 775s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '23' because it was < 2 characters long 775s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '35' because it was < 2 characters long 775s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '47' because it was < 2 characters long 775s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '49' because it was < 2 characters long 775s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '74' because it was < 2 characters long 775s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '78' because it was < 2 characters long 775s 85 reads; of these: 775s 85 (100.00%) were unpaired; of these: 775s 85 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s Read 50 alignments... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 0 alignments, 0 edits 775s --------------- 775s PASSED 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.1 775s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.2 775s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 3 775s Reference gaps introduced: 2 775s Read gaps introduced: 0 775s Rearrangements introduced: 1 775s Created read sampler 775s Sampling 74 reads 775s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 775s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 74 reference bases 775s *** Run 69 of 100 775s /usr/bin/bowtie2 --cp-ival 1 -D 13 --local --nofw --trim3 4 --score-min L,4.07484457565555,9.77939028630414 -a --cp-min 4 -R 2 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 775s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '13' because it was < 2 characters long 775s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '15' because it was < 2 characters long 775s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '16' because it was < 2 characters long 775s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '19' because it was < 2 characters long 775s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '22' because it was < 2 characters long 775s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '29' because it was < 2 characters long 775s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '39' because it was < 2 characters long 775s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '42' because it was < 2 characters long 775s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '44' because it was < 2 characters long 775s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '46' because it was < 2 characters long 775s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '48' because it was < 2 characters long 775s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '53' because it was < 2 characters long 775s 74 reads; of these: 775s 74 (100.00%) were unpaired; of these: 775s 74 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s Read 50 alignments... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 0 alignments, 0 edits 775s --------------- 775s PASSED 775s ALSO checking that bowtie2 and bowtie2-align match up 775s /usr/bin/bowtie2 --cp-ival 1 -D 13 --local --nofw --trim3 4 --score-min L,4.07484457565555,9.77939028630414 -a --cp-min 4 -R 2 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 775s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '13' because it was < 2 characters long 775s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '15' because it was < 2 characters long 775s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '16' because it was < 2 characters long 775s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '19' because it was < 2 characters long 775s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '22' because it was < 2 characters long 775s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '29' because it was < 2 characters long 775s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '39' because it was < 2 characters long 775s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '42' because it was < 2 characters long 775s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '44' because it was < 2 characters long 775s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '46' because it was < 2 characters long 775s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '48' because it was < 2 characters long 775s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '53' because it was < 2 characters long 775s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 775s 74 reads; of these: 775s 74 (100.00%) were unpaired; of these: 775s 74 (100.00%) aligned 0 times 775s 0 (0.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 0.00% overall alignment rate 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.1 775s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.2 775s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 6 775s Reference gaps introduced: 1 775s Read gaps introduced: 0 775s Rearrangements introduced: 3 775s Created read sampler 775s Sampling 35 reads 775s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 775s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 74 reference bases 775s *** Run 70 of 100 775s /usr/bin/bowtie2 --mp 4.28193230925326,2.95209239839011 --ma 15.0661448252491 --nofw --cp-ival 2 --cp-min 2 --rdg 43.5927310834556 --score-min L,5.69214509838835,6.43667776888125 --trim5 8 -i L,3.30635540049533 -a -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 775s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 775s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '5' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 775s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read '9' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 775s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '10' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 775s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '15' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 775s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '19' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 775s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '35' because it was < 2 characters long 775s 35 reads; of these: 775s 28 (80.00%) were paired; of these: 775s 28 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 28 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 28 pairs aligned 0 times concordantly or discordantly; of these: 775s 56 mates make up the pairs; of these: 775s 51 (91.07%) aligned 0 times 775s 5 (8.93%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 7 (20.00%) were unpaired; of these: 775s 6 (85.71%) aligned 0 times 775s 1 (14.29%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 9.52% overall alignment rate 775s Read 50 alignments... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s CAGTTACCTCCTGAA 775s CAGTTACCTCCTGAA 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s GAA 775s GAA 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s CAACG 775s CAACG 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s AACGCAGT 775s AACGCAGT 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s TAGACG 775s TAGACG 775s Processing line... 775s Processing line... 775s ACAACGCAGTTACCTCCTGAAAACATC 775s ACAACGCAGTTACCTCCTGAAAACATC 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 6 alignments, 0 edits 775s --------------- 775s PASSED 775s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 775s /usr/bin/bowtie2 --mp 4.28193230925326,2.95209239839011 --ma 15.0661448252491 --nofw --cp-ival 2 --cp-min 2 --rdg 43.5927310834556 --score-min L,5.69214509838835,6.43667776888125 --trim5 8 -i L,3.30635540049533 -a -q -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 775s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 775s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '5' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 775s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 775s Warning: skipping mate #2 of read '9' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 775s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '10' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 775s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '15' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 775s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '19' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 775s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '35' because it was < 2 characters long 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 775s 35 reads; of these: 775s 28 (80.00%) were paired; of these: 775s 28 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 28 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 28 pairs aligned 0 times concordantly or discordantly; of these: 775s 56 mates make up the pairs; of these: 775s 51 (91.07%) aligned 0 times 775s 5 (8.93%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 7 (20.00%) were unpaired; of these: 775s 6 (85.71%) aligned 0 times 775s 1 (14.29%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 9.52% overall alignment rate 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 775s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.1 775s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.2 775s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 4 775s Reference gaps introduced: 1 775s Read gaps introduced: 0 775s Rearrangements introduced: 1 775s Created read sampler 775s Sampling 25 reads 775s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 775s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 74 reference bases 775s *** Run 71 of 100 775s /usr/bin/bowtie2 -N 0 -L23 --ma 33.9163072774588 --cp-ival 1 --cp-min 12 --trim3 9 --rfg 27.142871762693,3.96844075355561 --rdg 11.0597578538952,17.3279826696396 --score-min L,7.04845986334565,1.11129021665997 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 775s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 775s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '5' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 775s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '6' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 775s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '19' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 775s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '20' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 775s 25 reads; of these: 775s 19 (76.00%) were paired; of these: 775s 19 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 19 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 19 pairs aligned 0 times concordantly or discordantly; of these: 775s 38 mates make up the pairs; of these: 775s 34 (89.47%) aligned 0 times 775s 3 (7.89%) aligned exactly 1 time 775s 1 (2.63%) aligned >1 times 775s 6 (24.00%) were unpaired; of these: 775s 5 (83.33%) aligned 0 times 775s 1 (16.67%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 11.36% overall alignment rate 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s AGTTACCTCCT 775s AGTTACCTCCT 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s CCTCCTGAAAACATC 775s CCTCCTGAAAACATC 775s Processing line... 775s Processing line... 775s Processing line... 775s AACAACGCAG 775s AACAACGCAG 775s Processing line... 775s Processing line... 775s TTACCTCCT 775s TTACCTCCT 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s ACA 775s ACA 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 5 alignments, 0 edits 775s --------------- 775s PASSED 775s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 775s /usr/bin/bowtie2 -N 0 -L23 --ma 33.9163072774588 --cp-ival 1 --cp-min 12 --trim3 9 --rfg 27.142871762693,3.96844075355561 --rdg 11.0597578538952,17.3279826696396 --score-min L,7.04845986334565,1.11129021665997 -f -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 775s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 775s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 775s *** Run 72 of 100 775s /usr/bin/bowtie2 --norc --trim5 9 --cp-min 3 -R 4 --rfg 46.1758547285328,7.66490884521848 --score-min L,6.12674133841554,1.63784185155135 -a --cp-ival 2 --local --mp 9.04688923060223,1.08279420064646 --trim3 7 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 775s /usr/bin/bowtie2 --norc --trim5 9 --cp-min 3 -R 4 --rfg 46.1758547285328,7.66490884521848 --score-min L,6.12674133841554,1.63784185155135 -a --cp-ival 2 --local --mp 9.04688923060223,1.08279420064646 --trim3 7 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 775s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '5' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 775s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '6' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 775s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '19' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 775s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 775s Warning: skipping mate #1 of read '20' because it was < 2 characters long 775s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 775s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 775s 25 reads; of these: 775s 19 (76.00%) were paired; of these: 775s 19 (100.00%) aligned concordantly 0 times 775s 0 (0.00%) aligned concordantly exactly 1 time 775s 0 (0.00%) aligned concordantly >1 times 775s ---- 775s 19 pairs aligned concordantly 0 times; of these: 775s 0 (0.00%) aligned discordantly 1 time 775s ---- 775s 19 pairs aligned 0 times concordantly or discordantly; of these: 775s 38 mates make up the pairs; of these: 775s 34 (89.47%) aligned 0 times 775s 3 (7.89%) aligned exactly 1 time 775s 1 (2.63%) aligned >1 times 775s 6 (24.00%) were unpaired; of these: 775s 5 (83.33%) aligned 0 times 775s 1 (16.67%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 11.36% overall alignment rate 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.2 775s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.1 775s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 4 775s Reference gaps introduced: 0 775s Read gaps introduced: 0 775s Rearrangements introduced: 1 775s Created read sampler 775s Sampling 70 reads 775s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 775s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 74 reference bases 775s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '1' because it was < 2 characters long 775s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '7' because it was < 2 characters long 775s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '8' because it was < 2 characters long 775s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '14' because it was < 2 characters long 775s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '16' because it was < 2 characters long 775s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '18' because it was < 2 characters long 775s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '19' because it was < 2 characters long 775s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '20' because it was < 2 characters long 775s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '21' because it was < 2 characters long 775s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '23' because it was < 2 characters long 775s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '28' because it was < 2 characters long 775s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '30' because it was < 2 characters long 775s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '33' because it was < 2 characters long 775s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '34' because it was < 2 characters long 775s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '37' because it was < 2 characters long 775s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '38' because it was < 2 characters long 775s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '40' because it was < 2 characters long 775s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '42' because it was < 2 characters long 775s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '43' because it was < 2 characters long 775s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '48' because it was < 2 characters long 775s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '51' because it was < 2 characters long 775s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '52' because it was < 2 characters long 775s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '54' because it was < 2 characters long 775s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '57' because it was < 2 characters long 775s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '59' because it was < 2 characters long 775s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '60' because it was < 2 characters long 775s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '61' because it was < 2 characters long 775s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '66' because it was < 2 characters long 775s 70 reads; of these: 775s 70 (100.00%) were unpaired; of these: 775s 68 (97.14%) aligned 0 times 775s 2 (2.86%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 2.86% overall alignment rate 775s Read 50 alignments... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s ACCTCCTGAAAACATCC 775s ACCTCCTGAAAACATCC 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s GAGATATGAGTGATTAATA 775s GAGATATGAGTGATTAATA 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s Processing line... 775s --- Summary --- 775s Read 1 reference strings 775s Checked 2 alignments, 0 edits 775s --------------- 775s PASSED 775s ALSO checking that bowtie2 and bowtie2-align match up 775s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '1' because it was < 2 characters long 775s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '7' because it was < 2 characters long 775s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '8' because it was < 2 characters long 775s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '14' because it was < 2 characters long 775s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '16' because it was < 2 characters long 775s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '18' because it was < 2 characters long 775s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '19' because it was < 2 characters long 775s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '20' because it was < 2 characters long 775s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '21' because it was < 2 characters long 775s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '23' because it was < 2 characters long 775s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '28' because it was < 2 characters long 775s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '30' because it was < 2 characters long 775s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '33' because it was < 2 characters long 775s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '34' because it was < 2 characters long 775s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '37' because it was < 2 characters long 775s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '38' because it was < 2 characters long 775s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '40' because it was < 2 characters long 775s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '42' because it was < 2 characters long 775s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '43' because it was < 2 characters long 775s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '48' because it was < 2 characters long 775s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '51' because it was < 2 characters long 775s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '52' because it was < 2 characters long 775s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '54' because it was < 2 characters long 775s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '57' because it was < 2 characters long 775s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '59' because it was < 2 characters long 775s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '60' because it was < 2 characters long 775s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '61' because it was < 2 characters long 775s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '66' because it was < 2 characters long 775s 70 reads; of these: 775s 70 (100.00%) were unpaired; of these: 775s 68 (97.14%) aligned 0 times 775s 2 (2.86%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 2.86% overall alignment rate 775s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 775s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 775s /usr/bin/bowtie2 --norc --trim5 9 --cp-min 3 -R 4 --rfg 46.1758547285328,7.66490884521848 --score-min L,6.12674133841554,1.63784185155135 -a --cp-ival 2 --local --mp 9.04688923060223,1.08279420064646 --trim3 7 -q -p 2 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 775s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '1' because it was < 2 characters long 775s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '7' because it was < 2 characters long 775s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '8' because it was < 2 characters long 775s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '14' because it was < 2 characters long 775s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '16' because it was < 2 characters long 775s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '18' because it was < 2 characters long 775s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '19' because it was < 2 characters long 775s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '20' because it was < 2 characters long 775s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '21' because it was < 2 characters long 775s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '23' because it was < 2 characters long 775s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '28' because it was < 2 characters long 775s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '30' because it was < 2 characters long 775s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '33' because it was < 2 characters long 775s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '34' because it was < 2 characters long 775s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '37' because it was < 2 characters long 775s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '38' because it was < 2 characters long 775s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '40' because it was < 2 characters long 775s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '42' because it was < 2 characters long 775s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '43' because it was < 2 characters long 775s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '48' because it was < 2 characters long 775s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '51' because it was < 2 characters long 775s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '52' because it was < 2 characters long 775s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '54' because it was < 2 characters long 775s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '57' because it was < 2 characters long 775s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '59' because it was < 2 characters long 775s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '60' because it was < 2 characters long 775s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '61' because it was < 2 characters long 775s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '66' because it was < 2 characters long 775s 70 reads; of these: 775s 70 (100.00%) were unpaired; of these: 775s 68 (97.14%) aligned 0 times 775s 2 (2.86%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 2.86% overall alignment rate 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 775s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 775s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 775s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 775s /usr/bin/bowtie2 --norc --trim5 9 --cp-min 3 -R 4 --rfg 46.1758547285328,7.66490884521848 --score-min L,6.12674133841554,1.63784185155135 -a --cp-ival 2 --local --mp 9.04688923060223,1.08279420064646 --trim3 7 -q -p 4 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 775s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '1' because it was < 2 characters long 775s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '7' because it was < 2 characters long 775s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '8' because it was < 2 characters long 775s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '14' because it was < 2 characters long 775s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '16' because it was < 2 characters long 775s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '18' because it was < 2 characters long 775s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '19' because it was < 2 characters long 775s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '20' because it was < 2 characters long 775s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 775s Warning: skipping read '21' because it was < 2 characters long 775s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '23' because it was < 2 characters long 775s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '28' because it was < 2 characters long 775s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '30' because it was < 2 characters long 775s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '33' because it was < 2 characters long 775s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '34' because it was < 2 characters long 775s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '37' because it was < 2 characters long 775s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '38' because it was < 2 characters long 775s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '40' because it was < 2 characters long 775s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '42' because it was < 2 characters long 775s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '43' because it was < 2 characters long 775s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '48' because it was < 2 characters long 775s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '51' because it was < 2 characters long 775s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '52' because it was < 2 characters long 775s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '54' because it was < 2 characters long 775s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '57' because it was < 2 characters long 775s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '59' because it was < 2 characters long 775s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '60' because it was < 2 characters long 775s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '61' because it was < 2 characters long 775s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 775s Warning: skipping read '66' because it was < 2 characters long 775s 70 reads; of these: 775s 70 (100.00%) were unpaired; of these: 775s 68 (97.14%) aligned 0 times 775s 2 (2.86%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 2.86% overall alignment rate 775s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 775s Flattened IUPAC characters 775s Mutating sequence Sim.pm.2 775s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutating sequence Sim.pm.1 775s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 775s Finished SNPs 775s Finished ref gaps 775s Finished read gaps 775s Mutated reference genome to subject genome 775s SNPs introduced: 4 775s Reference gaps introduced: 1 775s Read gaps introduced: 1 775s Rearrangements introduced: 0 775s Created read sampler 775s Sampling 62 reads 775s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 775s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 775s parsing sequence Sim.pm.1... 775s parsing sequence Sim.pm.2... 775s Parsed 74 reference bases 775s *** Run 73 of 100 775s /usr/bin/bowtie2 -N 0 -L12 --cp-ival 1 -D 31 -a --score-min L,8.71751849352805,2.45840141687734 --ma 14.4808915447797 --cp-min 3 -i S,0.508223222661286 --norc -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 775s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 776s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '18' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 776s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '22' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 776s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '31' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 776s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '40' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 776s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '41' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 776s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '49' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 776s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '54' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 776s 62 reads; of these: 776s 62 (100.00%) were paired; of these: 776s 62 (100.00%) aligned concordantly 0 times 776s 0 (0.00%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 62 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 62 pairs aligned 0 times concordantly or discordantly; of these: 776s 124 mates make up the pairs; of these: 776s 111 (89.52%) aligned 0 times 776s 10 (8.06%) aligned exactly 1 time 776s 3 (2.42%) aligned >1 times 776s 10.48% overall alignment rate 776s Read 50 alignments... 776s Read 100 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GTTACC 776s GTTACC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GTTACCTC 776s GTTACCTC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TT 776s TT 776s Processing line... 776s TT 776s TT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GCA 776s GCA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CCTCC 776s CCTCC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ATAG 776s ATAG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CAGTTACCT 776s CAGTTACCT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AT 776s AT 776s Processing line... 776s AT 776s AT 776s Processing line... 776s AT 776s AT 776s Processing line... 776s AT 776s AT 776s Processing line... 776s AT 776s AT 776s Processing line... 776s AT 776s AT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AG 776s AG 776s Processing line... 776s AG 776s AG 776s Processing line... 776s AG 776s AG 776s Processing line... 776s AG 776s AG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ACGA 776s ACGA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AACAT 776s AACAT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TCCTG 776s TCCTG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s /usr/bin/bowtie2 -N 0 -L12 --cp-ival 1 -D 31 -a --score-min L,8.71751849352805,2.45840141687734 --ma 14.4808915447797 --cp-min 3 -i S,0.508223222661286 --norc -f -p 2 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CAGTTA 776s CAGTTA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 22 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 776s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 776s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '18' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 776s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '22' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 776s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '31' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 776s Warning: skipping mate #1 of read '40' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '40' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 776s Warning: skipping mate #2 of read '41' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '41' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 776s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read '49' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 776s Warning: skipping mate #1 of read '54' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '54' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 776s 62 reads; of these: 776s 62 (100.00%) were paired; of these: 776s 62 (100.00%) aligned concordantly 0 times 776s 0 (0.00%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 62 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 62 pairs aligned 0 times concordantly or discordantly; of these: 776s 124 mates make up the pairs; of these: 776s 111 (89.52%) aligned 0 times 776s 10 (8.06%) aligned exactly 1 time 776s 3 (2.42%) aligned >1 times 776s 10.48% overall alignment rate 776s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.2 776s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.1 776s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 4 776s Reference gaps introduced: 1 776s Read gaps introduced: 0 776s Rearrangements introduced: 0 776s Created read sampler 776s Sampling 91 reads 776s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 776s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 74 reference bases 776s *** Run 74 of 100 776s /usr/bin/bowtie2 --gbar 1 --score-min L,5.06459519336493,1.37920254898826 --rdg 42.9112420815302,11.9897024827659 --mm --cp-ival 5 --local --nofw --mp 8.22793544101273,2.80482224906324 --trim3 2 -k 3 --trim5 8 --cp-min 4 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 776s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 776s Read 50 alignments... 776s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 776s Read 100 alignments... 776s 91 reads; of these: 776s 76 (83.52%) were paired; of these: 776s 76 (100.00%) aligned concordantly 0 times 776s 0 (0.00%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 76 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 76 pairs aligned 0 times concordantly or discordantly; of these: 776s 152 mates make up the pairs; of these: 776s 150 (98.68%) aligned 0 times 776s 2 (1.32%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 15 (16.48%) were unpaired; of these: 776s 14 (93.33%) aligned 0 times 776s 1 (6.67%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 1.80% overall alignment rate 776s Read 150 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TACCTCCTGAAAACA 776s TACCTCCTGAAAACA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CAGTTACCTCCTGAAAACA 776s CAGTTACCTCCTGAAAACA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AGTTACCTCCT 776s AGTTACCTCCT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 3 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 776s /usr/bin/bowtie2 --gbar 1 --score-min L,5.06459519336493,1.37920254898826 --rdg 42.9112420815302,11.9897024827659 --mm --cp-ival 5 --local --nofw --mp 8.22793544101273,2.80482224906324 --trim3 2 -k 3 --trim5 8 --cp-min 4 --qseq -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 776s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 776s 91 reads; of these: 776s 76 (83.52%) were paired; of these: 776s 76 (100.00%) aligned concordantly 0 times 776s 0 (0.00%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 76 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 76 pairs aligned 0 times concordantly or discordantly; of these: 776s 152 mates make up the pairs; of these: 776s 150 (98.68%) aligned 0 times 776s 2 (1.32%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 15 (16.48%) were unpaired; of these: 776s 14 (93.33%) aligned 0 times 776s 1 (6.67%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 1.80% overall alignment rate 776s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 776s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 776s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 776s /usr/bin/bowtie2 --gbar 1 --score-min L,5.06459519336493,1.37920254898826 --rdg 42.9112420815302,11.9897024827659 --mm --cp-ival 5 --local --nofw --mp 8.22793544101273,2.80482224906324 --trim3 2 -k 3 --trim5 8 --cp-min 4 --qseq -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 776s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 776s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 776s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 776s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 776s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 776s 91 reads; of these: 776s 76 (83.52%) were paired; of these: 776s 76 (100.00%) aligned concordantly 0 times 776s 0 (0.00%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 76 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 76 pairs aligned 0 times concordantly or discordantly; of these: 776s 152 mates make up the pairs; of these: 776s 150 (98.68%) aligned 0 times 776s 2 (1.32%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 15 (16.48%) were unpaired; of these: 776s 14 (93.33%) aligned 0 times 776s 1 (6.67%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 1.80% overall alignment rate 776s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.2 776s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.1 776s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 16 776s Reference gaps introduced: 0 776s Read gaps introduced: 1 776s Rearrangements introduced: 1 776s Created read sampler 776s Sampling 108 reads 776s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 776s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 74 reference bases 776s *** Run 75 of 100 776s /usr/bin/bowtie2 --trim3 1 -N 1 -L12 --cp-ival 1 -D 14 --cp-min 2 --mm --rfg 27.9074980524077,11.2616928397882 --rdg 2.29894985836499 --score-min L,1.09038814654713,4.9502272590852 --np 5 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 776s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 776s Warning: skipping read '15' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '15' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 776s Warning: skipping read '24' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '24' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 776s Warning: skipping read '34' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '34' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 776s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '38' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 776s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '42' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 776s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '49' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 776s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '57' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 776s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '63' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 776s Warning: skipping read '64' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '64' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 776s Warning: skipping read '67' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '67' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 776s Warning: skipping read '68' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '68' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 776s Warning: skipping read '72' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '72' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 776s Warning: skipping read '74' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '74' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 776s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '79' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 776s Warning: skipping read '97' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '97' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 776s Warning: skipping read '104' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '104' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 776s 108 reads; of these: 776s 108 (100.00%) were unpaired; of these: 776s 94 (87.04%) aligned 0 times 776s 6 (5.56%) aligned exactly 1 time 776s 8 (7.41%) aligned >1 times 776s 12.96% overall alignment rate 776s Read 50 alignments... 776s Read 100 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AGA 776s AGA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AGA 776s AGA 776s Processing line... 776s Processing line... 776s Processing line... 776s ACGCAGT 776s ACGCAGT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GAGTGATTAATA 776s GAGTGATTAATA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s /usr/bin/bowtie2 --trim3 1 -N 1 -L12 --cp-ival 1 -D 14 --cp-min 2 --mm --rfg 27.9074980524077,11.2616928397882 --rdg 2.29894985836499 --score-min L,1.09038814654713,4.9502272590852 --np 5 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 776s Processing line... 776s Processing line... 776s Processing line... 776s GATT 776s GATT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TA 776s TA 776s Processing line... 776s Processing line... 776s GC 776s GC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TA 776s TA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GTC 776s GTC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GATATGAGTGATTAATAAC 776s GATATGAGTGATTAATAAC 776s Processing line... 776s TACCT 776s TACCT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TGA 776s TGA 776s Processing line... 776s AA 776s AA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ACCGAG 776s ACCGAG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 14 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2-align match up 776s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 776s Warning: skipping read '15' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '15' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 776s Warning: skipping read '24' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '24' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 776s Warning: skipping read '34' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '34' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 776s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '38' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 776s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '42' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 776s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '49' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 776s Warning: skipping read '57' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '57' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 776s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '63' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 776s Warning: skipping read '64' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '64' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 776s Warning: skipping read '67' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '67' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 776s Warning: skipping read '68' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '68' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 776s Warning: skipping read '72' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '72' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 776s Warning: skipping read '74' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '74' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 776s Warning: skipping read '79' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '79' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 776s Warning: skipping read '97' because length (0) <= # seed mismatches (1) 776s Warning: skipping read '97' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 776s Warning: skipping read '104' because length (1) <= # seed mismatches (1) 776s Warning: skipping read '104' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 776s 108 reads; of these: 776s 108 (100.00%) were unpaired; of these: 776s 94 (87.04%) aligned 0 times 776s 6 (5.56%) aligned exactly 1 time 776s 8 (7.41%) aligned >1 times 776s 12.96% overall alignment rate 776s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.2 776s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.1 776s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 6 776s Reference gaps introduced: 1 776s Read gaps introduced: 0 776s Rearrangements introduced: 1 776s Created read sampler 776s Sampling 126 reads 776s *** Run 76 of 100 776s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 1.2436997821622,1.2850413363094 --mp 6.07973740891445,1.13751057101805 --nofw --gbar 6 --rdg 35.6214905343143,17.4543029268346 --score-min L,5.78139014608141,9.13431288647307 -a --mm --cp-min 2 --trim5 0 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 776s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 776s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 74 reference bases 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: skipping mate #2 of read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 776s Read 50 alignments... 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 776s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 776s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 776s Read 100 alignments... 776s Read 150 alignments... 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 776s Read 200 alignments... 776s 126 reads; of these: 776s 126 (100.00%) were paired; of these: 776s 123 (97.62%) aligned concordantly 0 times 776s 3 (2.38%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 123 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 123 pairs aligned 0 times concordantly or discordantly; of these: 776s 246 mates make up the pairs; of these: 776s 226 (91.87%) aligned 0 times 776s 13 (5.28%) aligned exactly 1 time 776s 7 (2.85%) aligned >1 times 776s 10.32% overall alignment rate 776s Read 250 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ACAT 776s ACAT 776s Processing line... 776s GCAG 776s GCAG 776s Processing line... 776s Processing line... 776s Processing line... 776s ACCTCCTGAAAAC 776s ACCTCCTGAAAAC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TACCTC 776s TACCTC 776s Processing line... 776s Processing line... 776s CA 776s CA 776s Processing line... 776s CA 776s CA 776s Processing line... 776s CA 776s CA 776s Processing line... 776s CA 776s CA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ACAACGCAGTTACCTCCT 776s ACAACGCAGTTACCTCCT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TGAAAA 776s TGAAAA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ATAGACGA 776s ATAGACGA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AG 776s AG 776s Processing line... 776s AG 776s AG 776s Processing line... 776s AG 776s AG 776s Processing line... 776s AG 776s AG 776s Processing line... 776s Processing line... 776s ATAGA 776s ATAGA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TAT 776s TAT 776s Processing line... 776s Processing line... 776s AACAACGCAGTTACCTCCTGAAAACATC 776s AACAACGCAGTTACCTCCTGAAAACATC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AAC 776s AAC 776s Processing line... 776s AAC 776s AAC 776s Processing line... 776s AAC 776s AAC 776s Processing line... 776s AAC 776s AAC 776s Processing line... 776s AAC 776s AAC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TCCTGAAAACA 776s TCCTGAAAACA 776s Processing line... 776s AGTT 776s AGTT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ATC 776s ATC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GCA 776s GCA 776s Processing line... 776s ACGCA 776s ACGCA 776s Processing line... 776s TATGAGTGATTAA 776s TATGAGTGATTAA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AAA 776s AAA 776s Processing line... 776s AAA 776s AAA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CTCCTGAA 776s CTCCTGAA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AGTG 776s AGTG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s AC 776s AC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GC 776s GC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TC 776s TC 776s Processing line... 776s TC 776s TC 776s Processing line... 776s TC 776s TC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 53 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 776s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 1.2436997821622,1.2850413363094 --mp 6.07973740891445,1.13751057101805 --nofw --gbar 6 --rdg 35.6214905343143,17.4543029268346 --score-min L,5.78139014608141,9.13431288647307 -a --mm --cp-min 2 --trim5 0 --qseq -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: skipping mate #2 of read 'R_1_1_1_46_46_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 776s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 776s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #2 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 776s 126 reads; of these: 776s 126 (100.00%) were paired; of these: 776s 123 (97.62%) aligned concordantly 0 times 776s 3 (2.38%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 123 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 123 pairs aligned 0 times concordantly or discordantly; of these: 776s 246 mates make up the pairs; of these: 776s 226 (91.87%) aligned 0 times 776s 13 (5.28%) aligned exactly 1 time 776s 7 (2.85%) aligned >1 times 776s 10.32% overall alignment rate 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.1 776s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.2 776s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 6 776s Reference gaps introduced: 0 776s Read gaps introduced: 0 776s Rearrangements introduced: 1 776s Created read sampler 776s Sampling 66 reads 776s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 776s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 74 reference bases 776s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 776s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 776s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 776s Warning: skipping read '56' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 776s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 776s Warning: skipping read '62' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 776s 66 reads; of these: 776s 66 (100.00%) were unpaired; of these: 776s 56 (84.85%) aligned 0 times 776s 9 (13.64%) aligned exactly 1 time 776s 1 (1.52%) aligned >1 times 776s 15.15% overall alignment rate 776s Read 50 alignments... 776s Processing line... 776s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 776s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 776s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 776s *** Run 77 of 100 776s /usr/bin/bowtie2 --cp-min 6 --ma 36.8258114150697 --np 2 --norc --cp-ival 2 --mp 9.46524813098186,6.60874156781614 -a --mm --score-min L,5.16257942319813,2.43452683041561 -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GTTACC 776s GTTACC 776s Processing line... 776s Processing line... 776s AACCGAGATATGAGTGATT 776s AACCGAGATATGAGTGATT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TAT 776s TAT 776s Processing line... 776s Processing line... 776s GAGTGATTAATA 776s GAGTGATTAATA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GAGTG 776s GAGTG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AAAACAT 776s AAAACAT 776s Processing line... 776s ATC 776s ATC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ATATGAGTGATTAATAACGTCT 776s ATATGAGTGATTAATAACGTCT 776s Processing line... 776s Processing line... 776s TC 776s TC 776s Processing line... 776s TC 776s TC 776s Processing line... 776s TC 776s TC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s /usr/bin/bowtie2 --cp-min 6 --ma 36.8258114150697 --np 2 --norc --cp-ival 2 --mp 9.46524813098186,6.60874156781614 -a --mm --score-min L,5.16257942319813,2.43452683041561 -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s GTTACC 776s GTTACC 776s --- Summary --- 776s Read 1 reference strings 776s Checked 12 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2-align match up 776s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 776s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 776s Warning: skipping read '56' because length (1) <= # seed mismatches (0) 776s Warning: skipping read '56' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 776s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 776s Warning: skipping read '62' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 776s 66 reads; of these: 776s 66 (100.00%) were unpaired; of these: 776s 56 (84.85%) aligned 0 times 776s 9 (13.64%) aligned exactly 1 time 776s 1 (1.52%) aligned >1 times 776s 15.15% overall alignment rate 776s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 776s *** Run 78 of 100 776s /usr/bin/bowtie2 --score-min L,1.92966203811638,3.28753764761644 --rfg 34.1475339026844 --rdg 19.2103290743558,3.34201830116639 --np 1 -N 1 -L14 --cp-min 8 --n-ceil 1.26797745576039,1.33538667462201 --cp-ival 3 -D 39 --trim3 6 --qseq -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.1 776s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.2 776s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 5 776s Reference gaps introduced: 1 776s Read gaps introduced: 0 776s Rearrangements introduced: 1 776s Created read sampler 776s Sampling 127 reads 776s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 776s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 74 reference bases 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (1) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (1) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_102_102_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_102_102_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (1) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_122_122_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_122_122_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 776s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (1) 776s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 776s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 776s 127 reads; of these: 776s 127 (100.00%) were unpaired; of these: 776s 110 (86.61%) aligned 0 times 776s 13 (10.24%) aligned exactly 1 time 776s 4 (3.15%) aligned >1 times 776s 13.39% overall alignment rate 776s Read 50 alignments... 776s Read 100 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AACAACGCAGTTACCTCCTGAA 776s AACAACGCAGTTACCTCCTGAA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TT 776s TT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CGCAGTTACCTCCTGAAAACA 776s CGCAGTTACCTCCTGAAAACA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ATCC 776s ATCC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ATAA 776s ATAA 776s Processing line... 776s Processing line... 776s Processing line... 776s AGT 776s AGT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ACCGAGATA 776s ACCGAGATA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s AA 776s AA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TGATT 776s TGATT 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ACAA 776s ACAA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TAACAACGCAGTTACCTCCTGAAAACATC 776s TAACAACGCAGTTACCTCCTGAAAACATC 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CTG 776s CTG 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s CGCAGTTACCTCCTGAAAACA 776s CGCAGTTACCTCCTGAAAACA 776s Processing line... 776s Processing line... 776s Processing line... 776s AACGCAGTTACCTCCTGAAAA 776s AACGCAGTTACCTCCTGAAAA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s TAATAA 776s TAATAA 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s ACAA 776s ACAA 776s Processing line... 776s Processing line... 776s Processing line... 776s ACAA 776s ACAA 776s --- Summary --- 776s Read 1 reference strings 776s Checked 17 alignments, 0 edits 776s --------------- 776s PASSED 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.1 776s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.2 776s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 14 776s Reference gaps introduced: 1 776s Read gaps introduced: 0 776s Rearrangements introduced: 0 776s Created read sampler 776s Sampling 105 reads 776s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 776s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 74 reference bases 776s *** Run 79 of 100 776s /usr/bin/bowtie2 --cp-ival 1 --local --n-ceil 0.240785544257039,0.201096892400289 --cp-min 2 --trim5 4 --mm --score-min L,9.76617079233961,3.68099514901852 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 776s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '3' because it was < 2 characters long 776s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '5' because it was < 2 characters long 776s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '10' because it was < 2 characters long 776s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '11' because it was < 2 characters long 776s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '17' because it was < 2 characters long 776s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '19' because it was < 2 characters long 776s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '24' because it was < 2 characters long 776s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '33' because it was < 2 characters long 776s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '48' because it was < 2 characters long 776s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '52' because it was < 2 characters long 776s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '53' because it was < 2 characters long 776s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '60' because it was < 2 characters long 776s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '67' because it was < 2 characters long 776s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '68' because it was < 2 characters long 776s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '70' because it was < 2 characters long 776s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '78' because it was < 2 characters long 776s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '79' because it was < 2 characters long 776s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '88' because it was < 2 characters long 776s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '89' because it was < 2 characters long 776s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '104' because it was < 2 characters long 776s 105 reads; of these: 776s 105 (100.00%) were unpaired; of these: 776s 105 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 0.00% overall alignment rate 776s Read 50 alignments... 776s Read 100 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s /usr/bin/bowtie2 --cp-ival 1 --local --n-ceil 0.240785544257039,0.201096892400289 --cp-min 2 --trim5 4 --mm --score-min L,9.76617079233961,3.68099514901852 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 0 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2-align match up 776s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '3' because it was < 2 characters long 776s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '5' because it was < 2 characters long 776s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '10' because it was < 2 characters long 776s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '11' because it was < 2 characters long 776s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '17' because it was < 2 characters long 776s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '19' because it was < 2 characters long 776s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '24' because it was < 2 characters long 776s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '33' because it was < 2 characters long 776s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '48' because it was < 2 characters long 776s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '52' because it was < 2 characters long 776s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '53' because it was < 2 characters long 776s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '60' because it was < 2 characters long 776s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '67' because it was < 2 characters long 776s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '68' because it was < 2 characters long 776s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '70' because it was < 2 characters long 776s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '78' because it was < 2 characters long 776s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '79' because it was < 2 characters long 776s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '88' because it was < 2 characters long 776s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '89' because it was < 2 characters long 776s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '104' because it was < 2 characters long 776s 105 reads; of these: 776s 105 (100.00%) were unpaired; of these: 776s 105 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 0.00% overall alignment rate 776s Flattened IUPAC characters 776s Mutating sequence Sim.pm.2 776s Introducing 2 SNPs, 2/0 ref/read gaps, and 0 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutating sequence Sim.pm.1 776s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 776s Introducing 2 SNPs, 1/0 ref/read gaps, and 1 rearrangements 776s Finished SNPs 776s Finished ref gaps 776s Finished read gaps 776s Mutated reference genome to subject genome 776s SNPs introduced: 4 776s Reference gaps introduced: 3 776s Read gaps introduced: 0 776s Rearrangements introduced: 1 776s Created read sampler 776s Sampling 60 reads 776s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 776s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 776s parsing sequence Sim.pm.1... 776s parsing sequence Sim.pm.2... 776s Parsed 74 reference bases 776s *** Run 80 of 100 776s /usr/bin/bowtie2 --trim5 9 -a --np 1 --score-min L,8.60722037992148,4.88700496237512 --cp-ival 2 --local --cp-min 4 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 776s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '2' because it was < 2 characters long 776s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '5' because it was < 2 characters long 776s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '8' because it was < 2 characters long 776s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '9' because it was < 2 characters long 776s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '10' because it was < 2 characters long 776s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '11' because it was < 2 characters long 776s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '22' because it was < 2 characters long 776s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '37' because it was < 2 characters long 776s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '41' because it was < 2 characters long 776s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '44' because it was < 2 characters long 776s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '49' because it was < 2 characters long 776s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 776s Warning: skipping read '50' because it was < 2 characters long 776s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '53' because it was < 2 characters long 776s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 776s Warning: skipping mate #1 of read '54' because it was < 2 characters long 776s 60 reads; of these: 776s 51 (85.00%) were paired; of these: 776s 51 (100.00%) aligned concordantly 0 times 776s 0 (0.00%) aligned concordantly exactly 1 time 776s 0 (0.00%) aligned concordantly >1 times 776s ---- 776s 51 pairs aligned concordantly 0 times; of these: 776s 0 (0.00%) aligned discordantly 1 time 776s ---- 776s 51 pairs aligned 0 times concordantly or discordantly; of these: 776s 102 mates make up the pairs; of these: 776s 102 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 9 (15.00%) were unpaired; of these: 776s 9 (100.00%) aligned 0 times 776s 0 (0.00%) aligned exactly 1 time 776s 0 (0.00%) aligned >1 times 776s 0.00% overall alignment rate 776s Read 50 alignments... 776s Read 100 alignments... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s Processing line... 776s --- Summary --- 776s Read 1 reference strings 776s Checked 0 alignments, 0 edits 776s --------------- 776s PASSED 776s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 776s /usr/bin/bowtie2 --trim5 9 -a --np 1 --score-min L,8.60722037992148,4.88700496237512 --cp-ival 2 --local --cp-min 4 -f -p 4 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 777s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '2' because it was < 2 characters long 777s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '5' because it was < 2 characters long 777s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '8' because it was < 2 characters long 777s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '9' because it was < 2 characters long 777s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '10' because it was < 2 characters long 777s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '11' because it was < 2 characters long 777s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '22' because it was < 2 characters long 777s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '37' because it was < 2 characters long 777s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '41' because it was < 2 characters long 777s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '44' because it was < 2 characters long 777s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '49' because it was < 2 characters long 777s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '50' because it was < 2 characters long 777s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '53' because it was < 2 characters long 777s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 777s Warning: skipping mate #1 of read '54' because it was < 2 characters long 777s 60 reads; of these: 777s 51 (85.00%) were paired; of these: 777s 51 (100.00%) aligned concordantly 0 times 777s 0 (0.00%) aligned concordantly exactly 1 time 777s 0 (0.00%) aligned concordantly >1 times 777s ---- 777s 51 pairs aligned concordantly 0 times; of these: 777s 0 (0.00%) aligned discordantly 1 time 777s ---- 777s 51 pairs aligned 0 times concordantly or discordantly; of these: 777s 102 mates make up the pairs; of these: 777s 102 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 9 (15.00%) were unpaired; of these: 777s 9 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 777s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.2 777s Introducing 6 SNPs, 1/0 ref/read gaps, and 1 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.1 777s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutated reference genome to subject genome 777s SNPs introduced: 10 777s Reference gaps introduced: 1 777s Read gaps introduced: 0 777s Rearrangements introduced: 1 777s Created read sampler 777s Sampling 177 reads 777s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 777s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 777s *** Run 81 of 100 777s /usr/bin/bowtie2 --trim3 9 -N 1 -L26 --local --cp-ival 1 -D 12 --n-ceil 0.526649243554653,1.42765213844852 -a --rdg 33.3584723637766 --rfg 8.6592010497265,1.94157479891268 --score-min L,6.33568379866571,2.44050983313626 --cp-min 2 --trim5 8 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 777s parsing sequence Sim.pm.1... 777s parsing sequence Sim.pm.2... 777s Parsed 74 reference bases 777s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '3' because it was < 2 characters long 777s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '4' because it was < 2 characters long 777s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '5' because it was < 2 characters long 777s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '10' because it was < 2 characters long 777s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '15' because it was < 2 characters long 777s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '17' because it was < 2 characters long 777s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '19' because it was < 2 characters long 777s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '27' because it was < 2 characters long 777s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '28' because it was < 2 characters long 777s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '31' because it was < 2 characters long 777s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '34' because it was < 2 characters long 777s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '35' because it was < 2 characters long 777s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '41' because it was < 2 characters long 777s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '43' because it was < 2 characters long 777s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '49' because it was < 2 characters long 777s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '50' because it was < 2 characters long 777s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '51' because it was < 2 characters long 777s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #2 of read '54' because it was < 2 characters long 777s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '58' because it was < 2 characters long 777s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '62' because it was < 2 characters long 777s Warning: skipping read '66' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '66' because it was < 2 characters long 777s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '76' because it was < 2 characters long 777s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '79' because it was < 2 characters long 777s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '81' because it was < 2 characters long 777s Warning: skipping mate #2 of read '82' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #2 of read '82' because it was < 2 characters long 777s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '88' because it was < 2 characters long 777s Warning: skipping mate #1 of read '90' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '90' because it was < 2 characters long 777s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '91' because it was < 2 characters long 777s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '92' because it was < 2 characters long 777s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '95' because it was < 2 characters long 777s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '101' because it was < 2 characters long 777s Warning: skipping read '102' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '102' because it was < 2 characters long 777s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '104' because it was < 2 characters long 777s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '108' because it was < 2 characters long 777s Warning: skipping read '109' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '109' because it was < 2 characters long 777s Warning: skipping mate #1 of read '124' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '124' because it was < 2 characters long 777s Warning: skipping mate #1 of read '128' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '128' because it was < 2 characters long 777s Warning: skipping mate #2 of read '133' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #2 of read '133' because it was < 2 characters long 777s Warning: skipping mate #1 of read '140' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '140' because it was < 2 characters long 777s Warning: skipping mate #1 of read '144' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '144' because it was < 2 characters long 777s Warning: skipping mate #1 of read '146' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '146' because it was < 2 characters long 777s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '148' because it was < 2 characters long 777s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '150' because it was < 2 characters long 777s Warning: skipping read '151' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '151' because it was < 2 characters long 777s Warning: skipping mate #1 of read '152' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '152' because it was < 2 characters long 777s Warning: skipping read '153' because length (1) <= # seed mismatches (1) 777s Warning: skipping read '153' because it was < 2 characters long 777s Warning: skipping mate #1 of read '154' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '154' because it was < 2 characters long 777s Warning: skipping mate #1 of read '157' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '157' because it was < 2 characters long 777s Read 50 alignments... 777s Read 100 alignments... 777s Warning: skipping read '160' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '160' because it was < 2 characters long 777s Warning: skipping mate #1 of read '161' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '161' because it was < 2 characters long 777s Warning: skipping mate #1 of read '164' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '164' because it was < 2 characters long 777s Warning: skipping mate #2 of read '166' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #2 of read '166' because it was < 2 characters long 777s Warning: skipping mate #1 of read '168' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '168' because it was < 2 characters long 777s Warning: skipping mate #1 of read '170' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #2 of read '170' because length (1) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '170' because it was < 2 characters long 777s Warning: skipping mate #2 of read '170' because it was < 2 characters long 777s Warning: skipping read '173' because length (0) <= # seed mismatches (1) 777s Warning: skipping read '173' because it was < 2 characters long 777s Warning: skipping mate #1 of read '174' because length (0) <= # seed mismatches (1) 777s Warning: skipping mate #1 of read '174' because it was < 2 characters long 777s Read 150 alignments... 777s 177 reads; of these: 777s 123 (69.49%) were paired; of these: 777s 123 (100.00%) aligned concordantly 0 times 777s 0 (0.00%) aligned concordantly exactly 1 time 777s 0 (0.00%) aligned concordantly >1 times 777s ---- 777s 123 pairs aligned concordantly 0 times; of these: 777s 0 (0.00%) aligned discordantly 1 time 777s ---- 777s 123 pairs aligned 0 times concordantly or discordantly; of these: 777s 246 mates make up the pairs; of these: 777s 246 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 54 (30.51%) were unpaired; of these: 777s 54 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s Read 200 alignments... 777s Read 250 alignments... 777s Read 300 alignments... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 0 alignments, 0 edits 777s --------------- 777s PASSED 777s *** Run 82 of 100 777s /usr/bin/bowtie2 --score-min L,9.41307759616133,2.10069885270642 --rfg 26.8118714797353 --rdg 11.5500498110215 --mp 7.99529802687482,2.93619493235674 --n-ceil 0.800139179458763,0.0191581193955802 --cp-ival 1 -D 4 --trim3 4 --norc -M 4 --trim5 6 --cp-min 2 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.2 777s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.1 777s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutated reference genome to subject genome 777s SNPs introduced: 9 777s Reference gaps introduced: 1 777s Read gaps introduced: 0 777s Rearrangements introduced: 0 777s Created read sampler 777s Sampling 149 reads 777s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 777s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 777s parsing sequence Sim.pm.1... 777s parsing sequence Sim.pm.2... 777s Parsed 74 reference bases 777s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '8' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '9' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '12' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 777s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '23' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 777s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '25' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 777s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '26' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 777s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '29' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 777s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 777s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '44' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 777s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '47' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 777s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '48' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 777s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '51' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 777s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '54' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 777s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '56' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 777s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '61' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 777s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '62' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 777s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '64' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 777s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '65' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 777s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '66' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 777s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '69' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 777s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '74' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 777s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '77' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 777s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '78' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 777s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '82' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 777s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '83' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 777s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '84' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 777s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '86' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 777s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '87' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 777s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '89' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 777s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '93' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 777s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '98' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 777s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '106' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 777s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '107' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 777s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '111' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 777s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '112' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 777s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '113' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 777s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '120' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 777s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '121' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 777s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '124' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 777s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '128' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 777s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '129' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 777s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '130' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 777s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '140' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 777s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '144' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 777s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '147' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 777s Warning: skipping read '149' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '149' because it was < 2 characters long 777s 149 reads; of these: 777s 149 (100.00%) were unpaired; of these: 777s 133 (89.26%) aligned 0 times 777s 8 (5.37%) aligned exactly 1 time 777s 8 (5.37%) aligned >1 times 777s 10.74% overall alignment rate 777s Read 50 alignments... 777s Read 100 alignments... 777s Read 150 alignments... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s CGT 777s CGT 777s Processing line... 777s Processing line... 777s GA 777s GA 777s Processing line... 777s GA 777s GA 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s /usr/bin/bowtie2 --score-min L,9.41307759616133,2.10069885270642 --rfg 26.8118714797353 --rdg 11.5500498110215 --mp 7.99529802687482,2.93619493235674 --n-ceil 0.800139179458763,0.0191581193955802 --cp-ival 1 -D 4 --trim3 4 --norc -M 4 --trim5 6 --cp-min 2 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s AGATATGAGTGATTA 777s AGATATGAGTGATTA 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s AACCGAGATATGA 777s AACCGAGATATGA 777s Processing line... 777s Processing line... 777s Processing line... 777s CA 777s CA 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GAGATATGAGTGATTAA 777s GAGATATGAGTGATTAA 777s Processing line... 777s Processing line... 777s CGC 777s CGC 777s Processing line... 777s CTG 777s CTG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s TA 777s TA 777s Processing line... 777s GA 777s GA 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s TA 777s TA 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s CCGAGATATGAGTGAT 777s CCGAGATATGAGTGAT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s AA 777s AA 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s CGCAG 777s CGCAG 777s Processing line... 777s Processing line... 777s CGT 777s CGT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 16 alignments, 0 edits 777s --------------- 777s PASSED 777s ALSO checking that bowtie2 and bowtie2-align match up 777s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '8' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '9' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '12' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 777s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '23' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 777s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '25' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 777s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '26' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 777s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '29' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 777s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 777s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '44' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 777s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '47' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 777s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '48' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 777s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '51' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 777s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '54' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 777s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '56' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 777s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '61' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 777s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '62' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 777s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '64' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 777s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '65' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 777s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '66' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 777s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '69' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 777s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '74' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 777s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '77' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 777s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '78' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 777s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '82' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 777s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '83' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 777s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '84' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 777s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '86' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 777s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '87' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 777s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '89' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 777s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '93' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 777s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '98' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 777s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '106' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 777s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '107' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 777s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '111' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 777s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '112' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 777s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '113' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 777s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '120' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 777s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '121' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 777s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '124' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 777s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '128' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 777s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '129' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 777s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '130' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 777s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '140' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 777s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '144' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 777s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '147' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 777s Warning: skipping read '149' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '149' because it was < 2 characters long 777s 149 reads; of these: 777s 149 (100.00%) were unpaired; of these: 777s 133 (89.26%) aligned 0 times 777s 8 (5.37%) aligned exactly 1 time 777s 8 (5.37%) aligned >1 times 777s 10.74% overall alignment rate 777s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 777s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 777s /usr/bin/bowtie2 --score-min L,9.41307759616133,2.10069885270642 --rfg 26.8118714797353 --rdg 11.5500498110215 --mp 7.99529802687482,2.93619493235674 --n-ceil 0.800139179458763,0.0191581193955802 --cp-ival 1 -D 4 --trim3 4 --norc -M 4 --trim5 6 --cp-min 2 -q -p 3 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 777s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '8' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '9' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '12' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 777s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '23' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 777s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '25' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 777s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '26' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 777s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '29' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 777s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 777s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '44' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 777s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '47' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 777s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '48' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 777s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '51' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 777s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '54' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 777s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '56' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 777s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '61' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 777s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '62' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 777s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '64' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 777s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '65' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 777s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '66' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 777s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '69' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 777s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '74' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 777s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '77' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 777s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '78' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 777s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '82' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 777s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '83' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 777s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '84' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 777s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '86' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 777s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '87' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 777s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '89' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 777s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '93' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 777s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '98' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 777s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '106' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 777s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '107' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 777s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '111' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 777s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '112' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 777s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '113' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 777s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '120' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 777s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '121' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 777s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '124' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 777s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '128' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 777s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '129' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 777s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '130' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 777s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '140' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 777s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '144' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 777s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '147' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 777s Warning: skipping read '149' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '149' because it was < 2 characters long 777s 149 reads; of these: 777s 149 (100.00%) were unpaired; of these: 777s 133 (89.26%) aligned 0 times 777s 8 (5.37%) aligned exactly 1 time 777s 8 (5.37%) aligned >1 times 777s 10.74% overall alignment rate 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 777s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 777s /usr/bin/bowtie2 --score-min L,9.41307759616133,2.10069885270642 --rfg 26.8118714797353 --rdg 11.5500498110215 --mp 7.99529802687482,2.93619493235674 --n-ceil 0.800139179458763,0.0191581193955802 --cp-ival 1 -D 4 --trim3 4 --norc -M 4 --trim5 6 --cp-min 2 -q -p 3 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 777s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 777s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '8' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '9' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '12' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 777s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '23' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 777s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '25' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 777s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '26' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 777s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '29' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 777s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 777s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '44' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 777s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '47' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 777s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '48' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 777s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '51' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 777s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '54' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 777s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '56' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 777s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '61' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 777s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '62' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 777s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '64' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 777s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '65' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 777s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '66' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 777s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '69' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 777s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '74' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 777s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '77' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 777s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '78' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 777s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '82' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 777s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '83' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 777s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '84' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 777s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '86' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 777s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '87' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 777s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '89' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 777s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '93' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 777s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '98' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 777s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '106' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 777s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '107' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 777s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '111' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 777s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '112' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 777s Warning: skipping read '113' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '113' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 777s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '120' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 777s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '121' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 777s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '124' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 777s Warning: skipping read '128' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '128' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 777s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '129' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 777s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '130' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 777s Warning: skipping read '140' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '140' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 777s Warning: skipping read '144' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '144' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 777s Warning: skipping read '147' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '147' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 777s Warning: skipping read '149' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '149' because it was < 2 characters long 777s 149 reads; of these: 777s 149 (100.00%) were unpaired; of these: 777s 133 (89.26%) aligned 0 times 777s 8 (5.37%) aligned exactly 1 time 777s 8 (5.37%) aligned >1 times 777s 10.74% overall alignment rate 777s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.2 777s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.1 777s Introducing 0 SNPs, 1/0 ref/read gaps, and 2 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutated reference genome to subject genome 777s SNPs introduced: 3 777s Reference gaps introduced: 2 777s Read gaps introduced: 0 777s Rearrangements introduced: 2 777s Created read sampler 777s Sampling 53 reads 777s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 777s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 777s parsing sequence Sim.pm.1... 777s *** Run 83 of 100 777s /usr/bin/bowtie2 --nofw --mp 6.13535569305775,1.26663813631248 -N 0 -L16 --cp-ival 1 --n-ceil 0.111149310575654,1.44953183676591 --mm --score-min L,5.75027798711026,1.55682751039524 --gbar 2 -R 1 --ma 23.9643934019718 --cp-min 2 --qseq -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq 777s parsing sequence Sim.pm.2... 777s Parsed 74 reference bases 777s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 777s 53 reads; of these: 777s 53 (100.00%) were unpaired; of these: 777s 46 (86.79%) aligned 0 times 777s 4 (7.55%) aligned exactly 1 time 777s 3 (5.66%) aligned >1 times 777s 13.21% overall alignment rate 777s Read 50 alignments... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GAA 777s GAA 777s Processing line... 777s Processing line... 777s Processing line... 777s ACCTCCTGAAAACAT 777s ACCTCCTGAAAACAT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s ACC 777s ACC 777s Processing line... 777s Processing line... 777s Processing line... 777s AACGCAGTTACC 777s AACGCAGTTACC 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s AAAAC 777s AAAAC 777s Processing line... 777s Processing line... 777s AT 777s AT 777s Processing line... 777s AG 777s AG 777s Processing line... 777s Processing line... 777s /usr/bin/bowtie2 --nofw --mp 6.13535569305775,1.26663813631248 -N 0 -L16 --cp-ival 1 --n-ceil 0.111149310575654,1.44953183676591 --mm --score-min L,5.75027798711026,1.55682751039524 --gbar 2 -R 1 --ma 23.9643934019718 --cp-min 2 --qseq -p 2 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 7 alignments, 0 edits 777s --------------- 777s PASSED 777s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 777s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 777s 53 reads; of these: 777s 53 (100.00%) were unpaired; of these: 777s 46 (86.79%) aligned 0 times 777s 4 (7.55%) aligned exactly 1 time 777s 3 (5.66%) aligned >1 times 777s 13.21% overall alignment rate 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 777s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 777s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 777s /usr/bin/bowtie2 --nofw --mp 6.13535569305775,1.26663813631248 -N 0 -L16 --cp-ival 1 --n-ceil 0.111149310575654,1.44953183676591 --mm --score-min L,5.75027798711026,1.55682751039524 --gbar 2 -R 1 --ma 23.9643934019718 --cp-min 2 --qseq -p 2 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 777s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 777s 53 reads; of these: 777s 53 (100.00%) were unpaired; of these: 777s 46 (86.79%) aligned 0 times 777s 4 (7.55%) aligned exactly 1 time 777s 3 (5.66%) aligned >1 times 777s 13.21% overall alignment rate 777s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.1 777s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.2 777s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s *** Run 84 of 100 777s /usr/bin/bowtie2 --trim5 5 -i S,2.69072769708552 --norc --np 7 --ma 9.63973839878001 --cp-min 2 -a --mm --rfg 46.815853201946,6.30754103052476 --rdg 5.96491988842291,3.51655268152569 --score-min L,4.92472579544489,3.24713531369646 --gbar 2 --nofw --cp-ival 1 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 777s Mutated reference genome to subject genome 777s SNPs introduced: 3 777s Reference gaps introduced: 1 777s Read gaps introduced: 0 777s Rearrangements introduced: 0 777s Created read sampler 777s Sampling 59 reads 777s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 777s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 777s parsing sequence Sim.pm.1... 777s parsing sequence Sim.pm.2... 777s Parsed 74 reference bases 777s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '1' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '6' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 777s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '22' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 777s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '33' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 777s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '35' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 777s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '41' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 777s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '44' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 777s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '53' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 777s 59 reads; of these: 777s 59 (100.00%) were unpaired; of these: 777s 59 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s Read 50 alignments... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 0 alignments, 0 edits 777s --------------- 777s PASSED 777s /usr/bin/bowtie2 --trim5 5 -i S,2.69072769708552 --norc --np 7 --ma 9.63973839878001 --cp-min 2 -a --mm --rfg 46.815853201946,6.30754103052476 --rdg 5.96491988842291,3.51655268152569 --score-min L,4.92472579544489,3.24713531369646 --gbar 2 --nofw --cp-ival 1 -q -p 4 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 777s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 777s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '1' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '6' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 777s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '22' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 777s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '33' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 777s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '35' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 777s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '41' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 777s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '44' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 777s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '53' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 777s 59 reads; of these: 777s 59 (100.00%) were unpaired; of these: 777s 59 (100.00%) aligned 0 times 777s 0 (0.00%) aligned exactly 1 time 777s 0 (0.00%) aligned >1 times 777s 0.00% overall alignment rate 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 777s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.1 777s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.2 777s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutated reference genome to subject genome 777s SNPs introduced: 5 777s Reference gaps introduced: 1 777s Read gaps introduced: 0 777s Rearrangements introduced: 0 777s Created read sampler 777s Sampling 121 reads 777s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 777s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 777s parsing sequence Sim.pm.1... 777s parsing sequence Sim.pm.2... 777s Parsed 74 reference bases 777s *** Run 85 of 100 777s /usr/bin/bowtie2 --mp 9.31182581954878,6.64365030997911 --cp-ival 2 --cp-min 2 -R 2 --norc --score-min L,6.08987211931456,9.48726421055266 --np 1 --mm --trim5 3 -q -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '3' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '6' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 777s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '14' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 777s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '17' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 777s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '29' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 777s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '35' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 777s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '37' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 777s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 777s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '59' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 777s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '65' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 777s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '66' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 777s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '79' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 777s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '85' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 777s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '86' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 777s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '102' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 777s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '106' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 777s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '111' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 777s Warning: skipping read '115' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '115' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 777s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '119' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 777s 121 reads; of these: 777s 121 (100.00%) were unpaired; of these: 777s 106 (87.60%) aligned 0 times 777s 9 (7.44%) aligned exactly 1 time 777s 6 (4.96%) aligned >1 times 777s 12.40% overall alignment rate 777s Read 50 alignments... 777s Read 100 alignments... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s AGATATGA 777s AGATATGA 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s TC 777s TC 777s Processing line... 777s GATTAATAACGTCTG 777s GATTAATAACGTCTG 777s Processing line... 777s Processing line... 777s Processing line... 777s TATGAGTGATTAATAACG 777s TATGAGTGATTAATAACG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s GATTAATAACGTCTG 777s GATTAATAACGTCTG 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s /usr/bin/bowtie2 --mp 9.31182581954878,6.64365030997911 --cp-ival 2 --cp-min 2 -R 2 --norc --score-min L,6.08987211931456,9.48726421055266 --np 1 --mm --trim5 3 -q -p 4 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 777s Processing line... 777s Processing line... 777s GAT 777s GAT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s TTACCTCC 777s TTACCTCC 777s Processing line... 777s Processing line... 777s ACCTCCTG 777s ACCTCCTG 777s Processing line... 777s Processing line... 777s TGAT 777s TGAT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s CT 777s CT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s AAT 777s AAT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s AC 777s AC 777s Processing line... 777s Processing line... 777s Processing line... 777s AT 777s AT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s TT 777s TT 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s Processing line... 777s AATAA 777s AATAA 777s Processing line... 777s --- Summary --- 777s Read 1 reference strings 777s Checked 15 alignments, 0 edits 777s --------------- 777s PASSED 777s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 777s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 777s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '3' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 777s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '6' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 777s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '14' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 777s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '17' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 777s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '29' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 777s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '35' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 777s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '37' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 777s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '40' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 777s Warning: skipping read '59' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '59' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 777s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '65' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 777s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '66' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 777s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '79' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 777s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '85' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 777s Warning: skipping read '86' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '86' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 777s Warning: skipping read '102' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '102' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 777s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '106' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 777s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '111' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 777s Warning: skipping read '115' because length (1) <= # seed mismatches (0) 777s Warning: skipping read '115' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 777s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 777s Warning: skipping read '119' because it was < 2 characters long 777s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 777s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 777s 121 reads; of these: 777s 121 (100.00%) were unpaired; of these: 777s 106 (87.60%) aligned 0 times 777s 9 (7.44%) aligned exactly 1 time 777s 6 (4.96%) aligned >1 times 777s 12.40% overall alignment rate 777s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 777s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 777s Flattened IUPAC characters 777s Mutating sequence Sim.pm.2 777s Introducing 2 SNPs, 1/0 ref/read gaps, and 2 rearrangements 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutating sequence Sim.pm.1 777s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 777s *** Run 86 of 100 777s /usr/bin/bowtie2 --rfg 37.8494275851181,19.5852686300631 --score-min L,4.43437001943656,6.61072803284595 --cp-ival 6 --local --n-ceil 0.538268929697973,0.0100058854327073 --trim3 8 --np 1 --trim5 4 --cp-min 2 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 777s Finished SNPs 777s Finished ref gaps 777s Finished read gaps 777s Mutated reference genome to subject genome 777s SNPs introduced: 5 777s Reference gaps introduced: 1 777s Read gaps introduced: 0 777s Rearrangements introduced: 4 777s Created read sampler 777s Sampling 164 reads 777s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 777s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 777s parsing sequence Sim.pm.1... 777s parsing sequence Sim.pm.2... 777s Parsed 74 reference bases 778s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '1' because it was < 2 characters long 778s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '2' because it was < 2 characters long 778s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '3' because it was < 2 characters long 778s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '4' because it was < 2 characters long 778s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '5' because it was < 2 characters long 778s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '6' because it was < 2 characters long 778s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '7' because it was < 2 characters long 778s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '8' because it was < 2 characters long 778s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '11' because it was < 2 characters long 778s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '13' because it was < 2 characters long 778s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '16' because it was < 2 characters long 778s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '22' because it was < 2 characters long 778s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '26' because it was < 2 characters long 778s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '27' because it was < 2 characters long 778s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '30' because it was < 2 characters long 778s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '32' because it was < 2 characters long 778s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '33' because it was < 2 characters long 778s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '34' because it was < 2 characters long 778s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '37' because it was < 2 characters long 778s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '38' because it was < 2 characters long 778s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '41' because it was < 2 characters long 778s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '42' because it was < 2 characters long 778s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '45' because it was < 2 characters long 778s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '51' because it was < 2 characters long 778s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '58' because it was < 2 characters long 778s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '59' because it was < 2 characters long 778s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '60' because it was < 2 characters long 778s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '67' because it was < 2 characters long 778s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '70' because it was < 2 characters long 778s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '72' because it was < 2 characters long 778s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '73' because it was < 2 characters long 778s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '77' because it was < 2 characters long 778s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '80' because it was < 2 characters long 778s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '82' because it was < 2 characters long 778s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '84' because it was < 2 characters long 778s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '87' because it was < 2 characters long 778s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '91' because it was < 2 characters long 778s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '95' because it was < 2 characters long 778s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '96' because it was < 2 characters long 778s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '97' because it was < 2 characters long 778s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '98' because it was < 2 characters long 778s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '99' because it was < 2 characters long 778s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '102' because it was < 2 characters long 778s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '103' because it was < 2 characters long 778s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '109' because it was < 2 characters long 778s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '111' because it was < 2 characters long 778s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '116' because it was < 2 characters long 778s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '117' because it was < 2 characters long 778s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '120' because it was < 2 characters long 778s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '125' because it was < 2 characters long 778s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '126' because it was < 2 characters long 778s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '127' because it was < 2 characters long 778s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '129' because it was < 2 characters long 778s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '130' because it was < 2 characters long 778s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '132' because it was < 2 characters long 778s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '138' because it was < 2 characters long 778s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '142' because it was < 2 characters long 778s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '143' because it was < 2 characters long 778s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '145' because it was < 2 characters long 778s Warning: skipping read '149' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '149' because it was < 2 characters long 778s Warning: skipping read '150' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '150' because it was < 2 characters long 778s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '152' because it was < 2 characters long 778s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '156' because it was < 2 characters long 778s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '158' because it was < 2 characters long 778s Warning: skipping read '161' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '161' because it was < 2 characters long 778s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '162' because it was < 2 characters long 778s 164 reads; of these: 778s 164 (100.00%) were unpaired; of these: 778s 164 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s Read 50 alignments... 778s Read 100 alignments... 778s Read 150 alignments... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s /usr/bin/bowtie2 --rfg 37.8494275851181,19.5852686300631 --score-min L,4.43437001943656,6.61072803284595 --cp-ival 6 --local --n-ceil 0.538268929697973,0.0100058854327073 --trim3 8 --np 1 --trim5 4 --cp-min 2 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s --- Summary --- 778s Read 1 reference strings 778s Checked 0 alignments, 0 edits 778s --------------- 778s PASSED 778s ALSO checking that bowtie2 and bowtie2-align match up 778s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '1' because it was < 2 characters long 778s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '2' because it was < 2 characters long 778s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '3' because it was < 2 characters long 778s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '4' because it was < 2 characters long 778s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '5' because it was < 2 characters long 778s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '6' because it was < 2 characters long 778s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '7' because it was < 2 characters long 778s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '8' because it was < 2 characters long 778s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '11' because it was < 2 characters long 778s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '13' because it was < 2 characters long 778s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '16' because it was < 2 characters long 778s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '22' because it was < 2 characters long 778s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '26' because it was < 2 characters long 778s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '27' because it was < 2 characters long 778s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '30' because it was < 2 characters long 778s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '32' because it was < 2 characters long 778s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '33' because it was < 2 characters long 778s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '34' because it was < 2 characters long 778s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '37' because it was < 2 characters long 778s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '38' because it was < 2 characters long 778s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '41' because it was < 2 characters long 778s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '42' because it was < 2 characters long 778s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '45' because it was < 2 characters long 778s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '51' because it was < 2 characters long 778s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '58' because it was < 2 characters long 778s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '59' because it was < 2 characters long 778s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '60' because it was < 2 characters long 778s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '67' because it was < 2 characters long 778s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '70' because it was < 2 characters long 778s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '72' because it was < 2 characters long 778s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '73' because it was < 2 characters long 778s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '77' because it was < 2 characters long 778s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '80' because it was < 2 characters long 778s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '82' because it was < 2 characters long 778s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '84' because it was < 2 characters long 778s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '87' because it was < 2 characters long 778s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '91' because it was < 2 characters long 778s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '95' because it was < 2 characters long 778s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '96' because it was < 2 characters long 778s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '97' because it was < 2 characters long 778s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '98' because it was < 2 characters long 778s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '99' because it was < 2 characters long 778s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '102' because it was < 2 characters long 778s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '103' because it was < 2 characters long 778s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '109' because it was < 2 characters long 778s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '111' because it was < 2 characters long 778s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '116' because it was < 2 characters long 778s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '117' because it was < 2 characters long 778s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '120' because it was < 2 characters long 778s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '125' because it was < 2 characters long 778s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '126' because it was < 2 characters long 778s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '127' because it was < 2 characters long 778s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '129' because it was < 2 characters long 778s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '130' because it was < 2 characters long 778s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '132' because it was < 2 characters long 778s Warning: skipping read '138' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '138' because it was < 2 characters long 778s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '142' because it was < 2 characters long 778s Warning: skipping read '143' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '143' because it was < 2 characters long 778s Warning: skipping read '145' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '145' because it was < 2 characters long 778s Warning: skipping read '149' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '149' because it was < 2 characters long 778s Warning: skipping read '150' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '150' because it was < 2 characters long 778s Warning: skipping read '152' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '152' because it was < 2 characters long 778s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '156' because it was < 2 characters long 778s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '158' because it was < 2 characters long 778s Warning: skipping read '161' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '161' because it was < 2 characters long 778s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '162' because it was < 2 characters long 778s 164 reads; of these: 778s 164 (100.00%) were unpaired; of these: 778s 164 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 778s Flattened IUPAC characters 778s Mutating sequence Sim.pm.1 778s Introducing 7 SNPs, 0/2 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutating sequence Sim.pm.2 778s Introducing 10 SNPs, 0/0 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutated reference genome to subject genome 778s SNPs introduced: 17 778s Reference gaps introduced: 0 778s Read gaps introduced: 2 778s Rearrangements introduced: 0 778s Created read sampler 778s Sampling 20 reads 778s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 778s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 778s parsing sequence Sim.pm.1... 778s parsing sequence Sim.pm.2... 778s Parsed 74 reference bases 778s *** Run 87 of 100 778s /usr/bin/bowtie2 --cp-min 3 -R 4 --np 4 --trim5 7 -M 5 --cp-ival 1 --local --mp 9.35445137793588,4.12090483274167 --nofw --score-min L,9.92009112714219,2.88518234912329 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 778s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 778s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '2' because it was < 2 characters long 778s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '4' because it was < 2 characters long 778s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '7' because it was < 2 characters long 778s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '15' because it was < 2 characters long 778s 20 reads; of these: 778s 15 (75.00%) were paired; of these: 778s 15 (100.00%) aligned concordantly 0 times 778s 0 (0.00%) aligned concordantly exactly 1 time 778s 0 (0.00%) aligned concordantly >1 times 778s ---- 778s 15 pairs aligned concordantly 0 times; of these: 778s 0 (0.00%) aligned discordantly 1 time 778s ---- 778s 15 pairs aligned 0 times concordantly or discordantly; of these: 778s 30 mates make up the pairs; of these: 778s 30 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 5 (25.00%) were unpaired; of these: 778s 5 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s --- Summary --- 778s Read 1 reference strings 778s Checked 0 alignments, 0 edits 778s --------------- 778s PASSED 778s Flattened IUPAC characters 778s Mutating sequence Sim.pm.1 778s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutating sequence Sim.pm.2 778s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutated reference genome to subject genome 778s SNPs introduced: 13 778s Reference gaps introduced: 0 778s Read gaps introduced: 0 778s Rearrangements introduced: 0 778s Created read sampler 778s Sampling 61 reads 778s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 778s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 778s parsing sequence Sim.pm.1... 778s parsing sequence Sim.pm.2... 778s Parsed 74 reference bases 778s *** Run 88 of 100 778s /usr/bin/bowtie2 --gbar 2 --score-min L,8.03199097035417,9.22882152230005 --norc -M 2 --cp-min 4 -D 18 --cp-ival 1 -N 0 -L15 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 778s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 778s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode fo/usr/bin/bowtie2 --gbar 2 --score-min L,8.03199097035417,9.22882152230005 --norc -M 2 --cp-min 4 -D 18 --cp-ival 1 -N 0 -L15 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 778s r mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 778s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 778s 61 reads; of these: 778s 61 (100.00%) were paired; of these: 778s 61 (100.00%) aligned concordantly 0 times 778s 0 (0.00%) aligned concordantly exactly 1 time 778s 0 (0.00%) aligned concordantly >1 times 778s ---- 778s 61 pairs aligned concordantly 0 times; of these: 778s 0 (0.00%) aligned discordantly 1 time 778s ---- 778s 61 pairs aligned 0 times concordantly or discordantly; of these: 778s 122 mates make up the pairs; of these: 778s 116 (95.08%) aligned 0 times 778s 3 (2.46%) aligned exactly 1 time 778s 3 (2.46%) aligned >1 times 778s 4.92% overall alignment rate 778s Read 50 alignments... 778s Read 100 alignments... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s TAA 778s TAA 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s AACGCAGTTAC 778s AACGCAGTTAC 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s TTAA 778s TTAA 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s TG 778s TG 778s Processing line... 778s Processing line... 778s AACAACGCAGTTACCTCC 778s AACAACGCAGTTACCTCC 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s CT 778s CT 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s --- Summary --- 778s Read 1 reference strings 778s Checked 6 alignments, 0 edits 778s --------------- 778s PASSED 778s ALSO checking that bowtie2 and bowtie2-align match up 778s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 778s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 778s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 778s 61 reads; of these: 778s 61 (100.00%) were paired; of these: 778s 61 (100.00%) aligned concordantly 0 times 778s 0 (0.00%) aligned concordantly exactly 1 time 778s 0 (0.00%) aligned concordantly >1 times 778s ---- 778s 61 pairs aligned concordantly 0 times; of these: 778s 0 (0.00%) aligned discordantly 1 time 778s ---- 778s 61 pairs aligned 0 times concordantly or discordantly; of these: 778s 122 mates make up the pairs; of these: 778s 116 (95.08%) aligned 0 times 778s 3 (2.46%) aligned exactly 1 time 778s 3 (2.46%) aligned >1 times 778s 4.92% overall alignment rate 778s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 778s /usr/bin/bowtie2 --gbar 2 --score-min L,8.03199097035417,9.22882152230005 --norc -M 2 --cp-min 4 -D 18 --cp-ival 1 -N 0 -L15 --qseq -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 778s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 778s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 778s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 778s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 778s 61 reads; of these: 778s 61 (100.00%) were paired; of these: 778s 61 (100.00%) aligned concordantly 0 times 778s 0 (0.00%) aligned concordantly exactly 1 time 778s 0 (0.00%) aligned concordantly >1 times 778s ---- 778s 61 pairs aligned concordantly 0 times; of these: 778s 0 (0.00%) aligned discordantly 1 time 778s ---- 778s 61 pairs aligned 0 times concordantly or discordantly; of these: 778s 122 mates make up the pairs; of these: 778s 116 (95.08%) aligned 0 times 778s 3 (2.46%) aligned exactly 1 time 778s 3 (2.46%) aligned >1 times 778s 4.92% overall alignment rate 778s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 778s Flattened IUPAC characters 778s Mutating sequence Sim.pm.1 778s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutating sequence Sim.pm.2 778s Introducing 3 SNPs, 0/2 ref/read gaps, and 1 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutated reference genome to subject genome 778s SNPs introduced: 6 778s Reference gaps introduced: 0 778s Read gaps introduced: 3 778s Rearrangements introduced: 1 778s Created read sampler 778s Sampling 148 reads 778s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 778s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 778s parsing sequence Sim.pm.1... 778s *** Run 89 of 100 778s /usr/bin/bowtie2 --score-min L,1.86888659924984,7.34301803221765 --rfg 10.277273773946,1.61044486513725 --mp 9.41521213170748,1.6278915178826 --local --cp-ival 3 --trim3 8 --np 1 -M 3 --cp-min 3 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 778s parsing sequence Sim.pm.2... 778s Parsed 74 reference bases 778s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 778s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '3' because it was < 2 characters long 778s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '8' because it was < 2 characters long 778s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '11' because it was < 2 characters long 778s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '18' because it was < 2 characters long 778s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read '20' because it was < 2 characters long 778s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '23' because it was < 2 characters long 778s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '24' because it was < 2 characters long 778s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '28' because it was < 2 characters long 778s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '43' because it was < 2 characters long 778s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '50' because it was < 2 characters long 778s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '54' because it was < 2 characters long 778s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '63' because it was < 2 characters long 778s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '64' because it was < 2 characters long 778s Read 50 alignments... 778s Read 100 alignments... 778s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '79' because it was < 2 characters long 778s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '80' because it was < 2 characters long 778s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '84' because it was < 2 characters long 778s Warning: skipping mate #1 of read '98' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '98' because it was < 2 characters long 778s Warning: skipping mate #1 of read '100' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '100' because it was < 2 characters long 778s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '106' because it was < 2 characters long 778s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '116' because it was < 2 characters long 778s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '125' because it was < 2 characters long 778s Warning: skipping mate #1 of read '127' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '127' because it was < 2 characters long 778s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '130' because it was < 2 characters long 778s Warning: skipping mate #1 of read '131' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '131' because it was < 2 characters long 778s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '138' because it was < 2 characters long 778s Warning: skipping mate #1 of read '141' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '141' because it was < 2 characters long 778s Read 150 alignments... 778s Read 200 alignments... 778s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read '148' because it was < 2 characters long 778s 148 reads; of these: 778s 126 (85.14%) were paired; of these: 778s 126 (100.00%) aligned concordantly 0 times 778s 0 (0.00%) aligned concordantly exactly 1 time 778s 0 (0.00%) aligned concordantly >1 times 778s ---- 778s 126 pairs aligned concordantly 0 times; of these: 778s 0 (0.00%) aligned discordantly 1 time 778s ---- 778s 126 pairs aligned 0 times concordantly or discordantly; of these: 778s 252 mates make up the pairs; of these: 778s 252 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 22 (14.86%) were unpaired; of these: 778s 22 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s Read 250 alignments... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing 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Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s --- Summary --- 778s Read 1 reference strings 778s Checked 0 alignments, 0 edits 778s --------------- 778s PASSED 778s Flattened IUPAC characters 778s Mutating sequence Sim.pm.1 778s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutating sequence Sim.pm.2 778s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutated reference genome to subject genome 778s SNPs introduced: 2 778s Reference gaps introduced: 0 778s Read gaps introduced: 1 778s Rearrangements introduced: 0 778s Created read sampler 778s Sampling 59 reads 778s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 778s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 778s parsing sequence Sim.pm.1... 778s *** Run 90 of 100 778s /usr/bin/bowtie2 --trim5 8 --norc --cp-min 7 --mm --rfg 25.2415252349012,18.066849230175 --score-min L,4.84100371388966,1.73990562506578 --mp 6.46650288656947,1.28865199467885 -N 1 -L21 --cp-ival 2 --local --n-ceil 1.45847158947498,0.359565418475801 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta 778s parsing sequence Sim.pm.2... 778s Parsed 74 reference bases 778s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '4' because it was < 2 characters long 778s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '7' because it was < 2 characters long 778s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '11' because it was < 2 characters long 778s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '13' because it was < 2 characters long 778s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '15' because it was < 2 characters long 778s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '18' because it was < 2 characters long 778s Warning: skipping read '19' because length (1) <= # seed mismatches (1) 778s Warning: skipping read '19' because it was < 2 characters long 778s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '22' because it was < 2 characters long 778s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '27' because it was < 2 characters long 778s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '28' because it was < 2 characters long 778s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '29' because it was < 2 characters long 778s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '30' because it was < 2 characters long 778s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '32' because it was < 2 characters long 778s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '35' because it was < 2 characters long 778s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '36' because it was < 2 characters long 778s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '46' because it was < 2 characters long 778s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '47' because it was < 2 characters long 778s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '49' because it was < 2 characters long 778s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 778s Warning: skipping read '51' because it was < 2 characters long 778s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '53' because it was < 2 characters long 778s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '58' because it was < 2 characters long 778s 59 reads; of these: 778s 59 (100.00%) were unpaired; of these: 778s 59 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s Read 50 alignments... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s /usr/bin/bowtie2 --trim5 8 --norc --cp-min 7 --mm --rfg 25.2415252349012,18.066849230175 --score-min L,4.84100371388966,1.73990562506578 --mp 6.46650288656947,1.28865199467885 -N 1 -L21 --cp-ival 2 --local --n-ceil 1.45847158947498,0.359565418475801 -f -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s --- Summary --- 778s Read 1 reference strings 778s Checked 0 alignments, 0 edits 778s --------------- 778s PASSED 778s ALSO checking that bowtie2 and bowtie2-align match up 778s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '4' because it was < 2 characters long 778s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '7' because it was < 2 characters long 778s Warning: skipping read '11' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '11' because it was < 2 characters long 778s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '13' because it was < 2 characters long 778s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '15' because it was < 2 characters long 778s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '18' because it was < 2 characters long 778s Warning: skipping read '19' because length (1) <= # seed mismatches (1) 778s Warning: skipping read '19' because it was < 2 characters long 778s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '22' because it was < 2 characters long 778s Warning: skipping read '27' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '27' because it was < 2 characters long 778s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '28' because it was < 2 characters long 778s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '29' because it was < 2 characters long 778s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '30' because it was < 2 characters long 778s Warning: skipping read '32' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '32' because it was < 2 characters long 778s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '35' because it was < 2 characters long 778s Warning: skipping read '36' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '36' because it was < 2 characters long 778s Warning: skipping read '46' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '46' because it was < 2 characters long 778s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '47' because it was < 2 characters long 778s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '49' because it was < 2 characters long 778s Warning: skipping read '51' because length (1) <= # seed mismatches (1) 778s Warning: skipping read '51' because it was < 2 characters long 778s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '53' because it was < 2 characters long 778s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 778s Warning: skipping read '58' because it was < 2 characters long 778s 59 reads; of these: 778s 59 (100.00%) were unpaired; of these: 778s 59 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 778s Flattened IUPAC characters 778s Mutating sequence Sim.pm.1 778s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutating sequence Sim.pm.2 778s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutated reference genome to subject genome 778s SNPs introduced: 10 778s Reference gaps introduced: 0 778s Read gaps introduced: 0 778s Rearrangements introduced: 0 778s Created read sampler 778s Sampling 74 reads 778s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 778s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 778s parsing sequence Sim.pm.1... 778s parsing sequence Sim.pm.2... 778s Parsed 74 reference bases 778s *** Run 91 of 100 778s /usr/bin/bowtie2 --np 1 --cp-min 2 --rfg 22.2976728078454,15.7805689505061 --score-min L,2.6835019700684,9.34283058119034 --gbar 1 --mm --mp 3.5967906260524,1.66043515928881 --n-ceil 1.38434244490653,0.882118889587049 --cp-ival 2 -D 16 --local --trim3 9 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq 778s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 778s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 778s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 778s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 778s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 778s Read 50 alignments... 778s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 778s Read 100 alignments... 778s 74 reads; of these: 778s 57 (77.03%) were paired; of these: 778s 57 (100.00%) aligned concordantly 0 times 778s 0 (0.00%) aligned concordantly exactly 1 time 778s 0 (0.00%) aligned concordantly >1 times 778s ---- 778s 57 pairs aligned concordantly 0 times; of these: 778s 0 (0.00%) aligned discordantly 1 time 778s ---- 778s 57 pairs aligned 0 times concordantly or discordantly; of these: 778s 114 mates make up the pairs; of these: 778s 114 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 17 (22.97%) were unpaired; of these: 778s 17 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s --- Summary --- 778s Read 1 reference strings 778s Checked 0 alignments, 0 edits 778s --------------- 778s PASSED 778s ALSO checking that bowtie2 and bowtie2-align match up 778s /usr/bin/bowtie2 --np 1 --cp-min 2 --rfg 22.2976728078454,15.7805689505061 --score-min L,2.6835019700684,9.34283058119034 --gbar 1 --mm --mp 3.5967906260524,1.66043515928881 --n-ceil 1.38434244490653,0.882118889587049 --cp-ival 2 -D 16 --local --trim3 9 --qseq -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 778s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 778s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 778s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 778s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 778s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 778s 74 reads; of these: 778s 57 (77.03%) were paired; of these: 778s 57 (100.00%) aligned concordantly 0 times 778s 0 (0.00%) aligned concordantly exactly 1 time 778s 0 (0.00%) aligned concordantly >1 times 778s ---- 778s 57 pairs aligned concordantly 0 times; of these: 778s 0 (0.00%) aligned discordantly 1 time 778s ---- 778s 57 pairs aligned 0 times concordantly or discordantly; of these: 778s 114 mates make up the pairs; of these: 778s 114 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 17 (22.97%) were unpaired; of these: 778s 17 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 778s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 778s /usr/bin/bowtie2 --np 1 --cp-min 2 --rfg 22.2976728078454,15.7805689505061 --score-min L,2.6835019700684,9.34283058119034 --gbar 1 --mm --mp 3.5967906260524,1.66043515928881 --n-ceil 1.38434244490653,0.882118889587049 --cp-ival 2 -D 16 --local --trim3 9 --qseq -p 4 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.qseq -2 /tmp/Sim.pm.fu45He6P_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 778s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 778s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 778s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 778s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 778s Warning: skipping mate #2 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 778s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 778s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 778s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 778s 74 reads; of these: 778s 57 (77.03%) were paired; of these: 778s 57 (100.00%) aligned concordantly 0 times 778s 0 (0.00%) aligned concordantly exactly 1 time 778s 0 (0.00%) aligned concordantly >1 times 778s ---- 778s 57 pairs aligned concordantly 0 times; of these: 778s 0 (0.00%) aligned discordantly 1 time 778s ---- 778s 57 pairs aligned 0 times concordantly or discordantly; of these: 778s 114 mates make up the pairs; of these: 778s 114 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 17 (22.97%) were unpaired; of these: 778s 17 (100.00%) aligned 0 times 778s 0 (0.00%) aligned exactly 1 time 778s 0 (0.00%) aligned >1 times 778s 0.00% overall alignment rate 778s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 778s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 778s Flattened IUPAC characters 778s Mutating sequence Sim.pm.1 778s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutating sequence Sim.pm.2 778s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutated reference genome to subject genome 778s SNPs introduced: 6 778s Reference gaps introduced: 0 778s Read gaps introduced: 0 778s Rearrangements introduced: 1 778s Created read sampler 778s Sampling 80 reads 778s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 778s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 778s parsing sequence Sim.pm.1... 778s parsing sequence Sim.pm.2... 778s Parsed 74 reference bases 778s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 778s *** Run 92 of 100 778s /usr/bin/bowtie2 --cp-min 5 --np 5 --trim5 3 --cp-ival 1 --mp 7.12083506037993,6.65747641068208 --trim3 8 --rfg 16.9938814535178,1.87818566879527 --score-min L,9.45878538163228,3.07719346068867 -a -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw 778s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 778s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '1' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 778s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '3' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 778s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '10' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 778s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '11' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 778s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '12' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 778s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '15' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 778s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '18' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 778s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '19' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 778s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '21' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 778s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '24' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 778s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '26' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 778s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '31' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 778s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '33' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 778s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '35' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 778s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '36' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 778s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '37' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 778s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 778s Warning: skipping read '38' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 778s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '40' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 778s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '41' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 778s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '42' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 778s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '49' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 778s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '52' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 778s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '53' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 778s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '55' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 778s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '56' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 778s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '70' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 778s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '73' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 778s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '74' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 778s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '75' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 778s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '76' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 778s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '77' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 778s 80 reads; of these: 778s 80 (100.00%) were unpaired; of these: 778s 73 (91.25%) aligned 0 times 778s 3 (3.75%) aligned exactly 1 time 778s 4 (5.00%) aligned >1 times 778s 8.75% overall alignment rate 778s Read 50 alignments... 778s Read 100 alignments... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s ATTAATAACG 778s ATTAATAACG 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s CCTCCTGAAAA 778s CCTCCTGAAAA 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s CCTCCTGAAAACATCC 778s CCTCCTGAAAACATCC 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s ACG 778s ACG 778s Processing line... 778s CGT 778s CGT 778s Processing line... 778s ACG 778s ACG 778s Processing line... 778s ACG 778s ACG 778s Processing line... 778s Processing line... 778s Processing line... 778s ACG 778s ACG 778s Processing line... 778s ACG 778s ACG 778s Processing line... 778s CGT 778s CGT 778s Processing line... 778s ACG 778s ACG 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s TC 778s TC 778s Processing line... 778s TC 778s TC 778s Processing line... 778s TC 778s TC 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s GA 778s GA 778s Processing line... 778s TC 778s TC 778s Processing line... 778s TC 778s TC 778s Processing line... 778s GA 778s GA 778s Processing line... 778s TC 778s TC 778s Processing line... 778s GA 778s GA 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s Processing line... 778s --- Summary --- 778s Read 1 reference strings 778s Checked 31 alignments, 0 edits 778s --------------- 778s PASSED 778s ALSO checking that bowtie2 and bowtie2-align match up 778s /usr/bin/bowtie2 --cp-min 5 --np 5 --trim5 3 --cp-ival 1 --mp 7.12083506037993,6.65747641068208 --trim3 8 --rfg 16.9938814535178,1.87818566879527 --score-min L,9.45878538163228,3.07719346068867 -a -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 778s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 778s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '1' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 778s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '3' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 778s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '10' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 778s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '11' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 778s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '12' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 778s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '15' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 778s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '18' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 778s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '19' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 778s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '21' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 778s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '24' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 778s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '26' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 778s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '31' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 778s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '33' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 778s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '35' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 778s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '36' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 778s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '37' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 778s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 778s Warning: skipping read '38' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 778s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '40' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 778s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '41' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 778s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '42' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 778s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '49' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 778s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '52' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 778s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '53' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 778s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '55' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 778s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '56' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 778s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '70' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 778s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '73' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 778s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '74' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 778s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '75' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 778s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '76' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 778s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 778s Warning: skipping read '77' because it was < 2 characters long 778s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 778s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 778s 80 reads; of these: 778s 80 (100.00%) were unpaired; of these: 778s 73 (91.25%) aligned 0 timesdiff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 778s 778s 3 (3.75%) aligned exactly 1 time 778s 4 (5.00%) aligned >1 times 778s 8.75% overall alignment rate 778s Flattened IUPAC characters 778s Mutating sequence Sim.pm.2 778s Introducing 10 SNPs, 1/0 ref/read gaps, and 1 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutating sequence Sim.pm.1 778s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 778s Finished SNPs 778s Finished ref gaps 778s Finished read gaps 778s Mutated reference genome to subject genome 778s SNPs introduced: 16 778s Reference gaps introduced: 1 778s Read gaps introduced: 1 778s Rearrangements introduced: 1 778s Created read sampler 778s Sampling 149 reads 778s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 778s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 778s parsing sequence Sim.pm.1... 778s parsing sequence Sim.pm.2... 778s Parsed 74 reference bases 778s *** Run 93 of 100 778s /usr/bin/bowtie2 --rfg 2.59293933091678 --score-min L,2.65414851885411,4.34128852840957 -k 2 --cp-ival 2 --local --cp-min 3 --nofw -R 4 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 779s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '15' because it was < 2 characters long 779s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '25' because it was < 2 characters long 779s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '30' because it was < 2 characters long 779s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '52' because it was < 2 characters long 779s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '70' because it was < 2 characters long 779s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '79' because it was < 2 characters long 779s Read 50 alignments... 779s Read 100 alignments... 779s Read 150 alignments... 779s Read 200 alignments... 779s 149 reads; of these: 779s 149 (100.00%) were paired; of these: 779s 149 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 149 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 149 pairs aligned 0 times concordantly or discordantly; of these: 779s 298 mates make up the pairs; of these: 779s 298 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s Read 250 alignments... 779s Read 300 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s 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line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 0 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 779s /usr/bin/bowtie2 --rfg 2.59293933091678 --score-min L,2.65414851885411,4.34128852840957 -k 2 --cp-ival 2 --local --cp-min 3 --nofw -R 4 -r -p 4 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 779s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '15' because it was < 2 characters long 779s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '25' because it was < 2 characters long 779s Warning: skipping mate #1 of read '30' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '30' because it was < 2 characters long 779s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '52' because it was < 2 characters long 779s Warning: skipping mate #2 of read '70' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '70' because it was < 2 characters long 779s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '79' because it was < 2 characters long 779s 149 reads; of these: 779s 149 (100.00%) were paired; of these: 779s 149 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 149 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 149 pairs aligned 0 times concordantly or discordantly; of these: 779s 298 mates make up the pairs; of these: 779s 298 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.1 779s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.2 779s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 9 779s Reference gaps introduced: 1 779s Read gaps introduced: 0 779s Rearrangements introduced: 1 779s Created read sampler 779s Sampling 63 reads 779s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fasta & /tmp/Sim.pm.fu45He6P_2.fasta 779s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 74 reference bases 779s *** Run 94 of 100 779s /usr/bin/bowtie2 --nofw --cp-ival 4 --local --trim3 3 --rdg 42.3750511365381,15.9829936155837 --rfg 8.42471290943241,18.6219486314178 --score-min L,3.3494650324362,5.98742874196332 --gbar 1 --mm --cp-min 4 -R 3 -f -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta 779s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '22' because it was < 2 characters long 779s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '24' because it was < 2 characters long 779s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '39' because it was < 2 characters long 779s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '47' because it was < 2 characters long 779s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '48' because it was < 2 characters long 779s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '50' because it was < 2 characters long 779s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '54' because it was < 2 characters long 779s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '57' because it was < 2 characters long 779s 63 reads; of these: 779s 55 (87.30%) were paired; of these: 779s 55 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 55 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 55 pairs aligned 0 times concordantly or discordantly; of these: 779s 110 mates make up the pairs; of these: 779s 110 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 8 (12.70%) were unpaired; of these: 779s 8 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s Read 50 alignments... 779s Read 100 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 0 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 779s /usr/bin/bowtie2 --nofw --cp-ival 4 --local --trim3 3 --rdg 42.3750511365381,15.9829936155837 --rfg 8.42471290943241,18.6219486314178 --score-min L,3.3494650324362,5.98742874196332 --gbar 1 --mm --cp-min 4 -R 3 -f -p 4 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fasta -2 /tmp/Sim.pm.fu45He6P_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 779s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '22' because it was < 2 characters long 779s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '24' because it was < 2 characters long 779s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '39' because it was < 2 characters long 779s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '47' because it was < 2 characters long 779s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '48' because it was < 2 characters long 779s Warning: skipping mate #1 of read '50' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '50' because it was < 2 characters long 779s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '54' because it was < 2 characters long 779s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 779s Warning: skipping read '57' because it was < 2 characters long 779s 63 reads; of these: 779s 55 (87.30%) were paired; of these: 779s 55 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 55 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 55 pairs aligned 0 times concordantly or discordantly; of these: 779s 110 mates make up the pairs; of these: 779s 110 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 8 (12.70%) were unpaired; of these: 779s 8 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 779s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 2 779s Reference gaps introduced: 0 779s Read gaps introduced: 2 779s Rearrangements introduced: 0 779s Created read sampler 779s Sampling 43 reads 779s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 779s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 74 reference bases 779s *** Run 95 of 100 779s /usr/bin/bowtie2 --trim5 0 --cp-min 10 --ma 17.7317231712846 --gbar 5 --score-min L,1.73571877206494,1.86003872058508 --rfg 15.6317687084434,5.51432101275646 --trim3 6 --cp-ival 1 --nofw --mp 9.27302995287234,1.5770580307813 -N 1 --qseq -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s 43 reads; of these: 779s 43 (100.00%) were unpaired; of these: 779s 34 (79.07%) aligned 0 times 779s 3 (6.98%) aligned exactly 1 time 779s 6 (13.95%) aligned >1 times 779s 20.93% overall alignment rate 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AGTGATTAATAACGT 779s AGTGATTAATAACGT 779s Processing line... 779s GAG 779s GAG 779s Processing line... 779s CGT 779s CGT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TTAC 779s TTAC 779s Processing line... 779s Processing line... 779s Processing line... 779s AT 779s AT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AC 779s AC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AT 779s AT 779s Processing line... 779s AT 779s AT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AT 779s AT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 9 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 779s /usr/bin/bowtie2 --trim5 0 --cp-min 10 --ma 17.7317231712846 --gbar 5 --score-min L,1.73571877206494,1.86003872058508 --rfg 15.6317687084434,5.51432101275646 --trim3 6 --cp-ival 1 --nofw --mp 9.27302995287234,1.5770580307813 -N 1 --qseq -p 3 -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 779s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (1) 779s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 779s 43 reads; of these: 779s 43 (100.00%) were unpaired; of these: 779s 34 (79.07%) aligned 0 times 779s 3 (6.98%) aligned exactly 1 time 779s 6 (13.95%) aligned >1 times 779s 20.93% overall alignment rate 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 779s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 8 779s Reference gaps introduced: 0 779s Read gaps introduced: 0 779s Rearrangements introduced: 0 779s Created read sampler 779s *** Run 96 of 100 779s /usr/bin/bowtie2 --mm -i S,1.71154577959394 -M 5 --np 2 --score-min L,2.96627928974747,7.4496882652042 --cp-ival 1 --cp-min 2 --mp 8.85828339725458,5.70468805539351 --ma 6.52782216708403 -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw 779s Sampling 74 reads 779s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 779s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 74 reference bases 779s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 779s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 779s Warning: skipping read '21' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 779s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 779s Warning: skipping read '58' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 779s 74 reads; of these: 779s 74 (100.00%) were unpaired; of these: 779s 61 (82.43%) aligned 0 times 779s 10 (13.51%) aligned exactly 1 time 779s 3 (4.05%) aligned >1 times 779s 17.57% overall alignment rate 779s Read 50 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CAACGCAGTTACCTC 779s CAACGCAGTTACCTC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GTC 779s GTC 779s Processing line... 779s TACCTCCTGAAAACAT 779s TACCTCCTGAAAACAT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AGATA 779s AGATA 779s Processing line... 779s AATAACGTCTG 779s AATAACGTCTG 779s Processing line... 779s Processing line... 779s Processing line... 779s GA 779s GA 779s Processing line... 779s Processing line... 779s CTCC 779s CTCC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CAGTTACCTCCTGAA 779s CAGTTACCTCCTGAA 779s Processing line... 779s ACAA 779s ACAA 779s Processing line... 779s CCTG 779s CCTG 779s Processing line... 779s Processing line... 779s Processing line... 779s AC 779s AC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CCTGAA 779s CCTGAA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AATAACGTC 779s AATAACGTC 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 13 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2-align match up 779s /usr/bin/bowtie2 --mm -i S,1.71154577959394 -M 5 --np 2 --score-min L,2.96627928974747,7.4496882652042 --cp-ival 1 --cp-min 2 --mp 8.85828339725458,5.70468805539351 --ma 6.52782216708403 -r -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.als 779s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 779s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 779s Warning: skipping read '21' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 779s Warning: skipping read '58' because length (1) <= # seed mismatches (0) 779s Warning: skipping read '58' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 779s 74 reads; of these: 779s 74 (100.00%) were unpaired; of these: 779s 61 (82.43%) aligned 0 times 779s 10 (13.51%) aligned exactly 1 time 779s 3 (4.05%) aligned >1 times 779s 17.57% overall alignment rate 779s diff -uw /tmp/Sim.pm.fu45He6P.als /tmp/Sim.pm.fu45He6P.debug.als 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 15 779s Reference gaps introduced: 0 779s Read gaps introduced: 1 779s Rearrangements introduced: 0 779s Created read sampler 779s Sampling 102 reads 779s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 779s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 74 reference bases 779s *** Run 97 of 100 779s /usr/bin/bowtie2 --cp-ival 5 --cp-min 2 --mp 4.40642541951787,3.3180682826954 --trim3 3 --rfg 12.0405339819591,6.67456371213213 --rdg 35.3857880289629,8.47056423919181 --norc --score-min L,4.72083594243557,4.05624946103487 -k 2 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 779s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '35' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 779s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '52' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 779s Read 50 alignments... 779s Read 100 alignments... 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 779s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '73' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 779s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '87' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 779s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '99' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 779s 102 reads; of these: 779s 96 (94.12%) were paired; of these: 779s 95 (98.96%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 1 (1.04%) aligned concordantly >1 times 779s ---- 779s 95 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 95 pairs aligned 0 times concordantly or discordantly; of these: 779s 190 mates make up the pairs; of these: 779s 179 (94.21%) aligned 0 times 779s 6 (3.16%) aligned exactly 1 time 779s 5 (2.63%) aligned >1 times 779s 6 (5.88%) were unpaired; of these: 779s 6 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 6.57% overall alignment rate 779s Read 150 alignments... 779s Read 200 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CGA 779s CGA 779s Processing line... 779s CGA 779s CGA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TGA 779s TGA 779s Processing line... 779s TGA 779s TGA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AC 779s AC 779s Processing line... 779s AC 779s AC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TAACAACG 779s TAACAACG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AACAACGCAGTTAC 779s AACAACGCAGTTAC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TTAC 779s TTAC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GCAGTT 779s GCAGTT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TAA 779s TAA 779s Processing line... 779s TAA 779s TAA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AA 779s AA 779s Processing line... 779s AACAACGCAGTTACC 779s AACAACGCAGTTACC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TT 779s TT 779s Processing line... 779s TT 779s TT 779s Processing line... 779s AACGCAGTTAC 779s AACGCAGTTAC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CCGAGATATGAGTGAT 779s CCGAGATATGAGTGAT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 18 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 779s /usr/bin/bowtie2 --cp-ival 5 --cp-min 2 --mp 4.40642541951787,3.3180682826954 --trim3 3 --rfg 12.0405339819591,6.67456371213213 --rdg 35.3857880289629,8.47056423919181 --norc --score-min L,4.72083594243557,4.05624946103487 -k 2 -q -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 779s Warning: skipping mate #2 of read '35' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '35' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 779s Warning: skipping mate #1 of read '52' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '52' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 779s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '73' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 779s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '87' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 779s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '99' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 779s 102 reads; of these: 779s 96 (94.12%) were paired; of these: 779s 95 (98.96%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 1 (1.04%) aligned concordantly >1 times 779s ---- 779s 95 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 95 pairs aligned 0 times concordantly or discordantly; of these: 779s 190 mates make up the pairs; of these: 779s 179 (94.21%) aligned 0 times 779s 6 (3.16%) aligned exactly 1 time 779s 5 (2.63%) aligned >1 times 779s 6 (5.88%) were unpaired; of these: 779s 6 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 6.57% overall alignment rate 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 779s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 3 SNPs, 2/0 ref/read gaps, and 1 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 9 779s Reference gaps introduced: 2 779s Read gaps introduced: 0 779s Rearrangements introduced: 2 779s Created read sampler 779s Sampling 51 reads 779s *** Run 98 of 100 779s /usr/bin/bowtie2 --rdg 17.1675430495484 --score-min L,3.00764444873192,4.38526485988289 --mm -a --cp-ival 2 --cp-min 11 -N 0 -L16 --ma 5.8726769192971 -q -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq 779s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.fastq & /tmp/Sim.pm.fu45He6P_2.fastq 779s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 74 reference bases 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 779s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '33' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 779s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '45' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 779s Read 50 alignments... 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 779s Read 100 alignments... 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 779s 51 reads; of these: 779s 51 (100.00%) were paired; of these: 779s 51 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 51 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 51 pairs aligned 0 times concordantly or discordantly; of these: 779s 102 mates make up the pairs; of these: 779s 85 (83.33%) aligned 0 times 779s 9 (8.82%) aligned exactly 1 time 779s 8 (7.84%) aligned >1 times 779s 16.67% overall alignment rate 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AACAT 779s AACAT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CTGAAAACAT 779s CTGAAAACAT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AA 779s AA 779s Processing line... 779s AA 779s AA 779s Processing line... 779s AA 779s AA 779s Processing line... 779s AA 779s AA 779s Processing line... 779s AA 779s AA 779s Processing line... 779s AA 779s AA 779s Processing line... 779s AA 779s AA 779s Processing line... 779s AA 779s AA 779s Processing line... 779s TT 779s TT 779s Processing line... 779s TT 779s TT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s ATAGACG 779s ATAGACG 779s Processing line... 779s Processing line... 779s CCTGAAAACA 779s CCTGAAAACA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CCTCCTGAAA 779s CCTCCTGAAA 779s Processing line... 779s Processing line... 779s CA 779s CA 779s Processing line... 779s TG 779s TG 779s Processing line... 779s CA 779s CA 779s Processing line... 779s CA 779s CA 779s Processing line... 779s TG 779s TG 779s Processing line... 779s TG 779s TG 779s Processing line... 779s TG 779s TG 779s Processing line... 779s CA 779s CA 779s Processing line... 779s Processing line... 779s GAT 779s GAT 779s Processing line... 779s GAT 779s GAT 779s Processing line... 779s ATC 779s ATC 779s Processing line... 779s Processing line... 779s TACCTCCTGAA 779s TACCTCCTGAA 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s GTT 779s GTT 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s TG 779s TG 779s Processing line... 779s CA 779s CA 779s Processing line... 779s TG 779s TG 779s Processing line... 779s CA 779s CA 779s Processing line... 779s CA 779s CA 779s Processing line... 779s TG 779s TG 779s Processing line... 779s CA 779s CA 779s Processing line... 779s TG 779s TG 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s ATAAC 779s ATAAC 779s Processing line... 779s Processing line... 779s GAT 779s GAT 779s Processing line... 779s GAT 779s GAT 779s Processing line... 779s ATC 779s ATC 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s AAC 779s AAC 779s Processing line... 779s GTT 779s GTT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CAGTTACCT 779s CAGTTACCT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s CT 779s CT 779s Processing line... 779s AG 779s AG 779s Processing line... 779s CT 779s CT 779s Processing line... 779s AG 779s AG 779s Processing line... 779s AG 779s AG 779s Processing line... 779s AG 779s AG 779s Processing line... 779s CT 779s CT 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s ATAA 779s ATAA 779s Processing line... 779s Processing line... 779s Processing line... 779s --- Summary --- 779s Read 1 reference strings 779s Checked 60 alignments, 0 edits 779s --------------- 779s PASSED 779s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 779s /usr/bin/bowtie2 --rdg 17.1675430495484 --score-min L,3.00764444873192,4.38526485988289 --mm -a --cp-ival 2 --cp-min 11 -N 0 -L16 --ma 5.8726769192971 -q -p 2 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 779s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '33' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 779s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '45' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 779s 51 reads; of these: 779s 51 (100.00%) were paired; of these: 779s 51 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 51 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 51 pairs aligned 0 times concordantly or discordantly; of these: 779s 102 mates make up the pairs; of these: 779s 85 (83.33%) aligned 0 times 779s 9 (8.82%) aligned exactly 1 time 779s 8 (7.84%) aligned >1 times 779s 16.67% overall alignment rate 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 779s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 779s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 779s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 779s /usr/bin/bowtie2 --rdg 17.1675430495484 --score-min L,3.00764444873192,4.38526485988289 --mm -a --cp-ival 2 --cp-min 11 -N 0 -L16 --ma 5.8726769192971 -q -p 3 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.fastq -2 /tmp/Sim.pm.fu45He6P_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 779s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 779s Warning: skipping mate #1 of read '33' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #1 of read '33' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 779s Warning: skipping mate #2 of read '45' because length (1) <= # seed mismatches (0) 779s Warning: skipping mate #2 of read '45' because it was < 2 characters long 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 779s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 779s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 779s 51 reads; of these: 779s 51 (100.00%) were paired; of these: 779s 51 (100.00%) aligned concordantly 0 times 779s 0 (0.00%) aligned concordantly exactly 1 time 779s 0 (0.00%) aligned concordantly >1 times 779s ---- 779s 51 pairs aligned concordantly 0 times; of these: 779s 0 (0.00%) aligned discordantly 1 time 779s ---- 779s 51 pairs aligned 0 times concordantly or discordantly; of these: 779s 102 mates make up the pairs; of these: 779s 85 (83.33%) aligned 0 times 779s 9 (8.82%) aligned exactly 1 time 779s 8 (7.84%) aligned >1 times 779s 16.67% overall alignment rate 779s Flattened IUPAC characters 779s Mutating sequence Sim.pm.2 779s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutating sequence Sim.pm.1 779s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 779s Finished SNPs 779s Finished ref gaps 779s Finished read gaps 779s Mutated reference genome to subject genome 779s SNPs introduced: 8 779s Reference gaps introduced: 1 779s Read gaps introduced: 1 779s Rearrangements introduced: 0 779s Created read sampler 779s Sampling 168 reads 779s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.qseq & /tmp/Sim.pm.fu45He6P_2.qseq 779s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 779s parsing sequence Sim.pm.1... 779s parsing sequence Sim.pm.2... 779s Parsed 74 reference bases 779s *** Run 99 of 100 779s /usr/bin/bowtie2 --score-min L,7.50212977439213,6.89018979001145 --rfg 10.015147619549 --gbar 1 --trim3 5 --mp 7.30187690055908,5.82006667540673 --cp-ival 1 -D 17 --local -M 4 --trim5 6 --cp-min 3 --qseq -x /tmp/Sim.pm.fu45He6P /tmp/Sim.pm.fu45He6P_1.qseq 779s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 779s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_159_159_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_159_159_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (1) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_163_163_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 779s Warning: skipping read 'R_1_1_1_165_165_1/1' because length (0) <= # seed mismatches (0) 779s Warning: skipping read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 779s 168 reads; of these: 779s 168 (100.00%) were unpaired; of these: 779s 168 (100.00%) aligned 0 times 779s 0 (0.00%) aligned exactly 1 time 779s 0 (0.00%) aligned >1 times 779s 0.00% overall alignment rate 779s Read 50 alignments... 779s Read 100 alignments... 779s Read 150 alignments... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 779s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 0 alignments, 0 edits 780s --------------- 780s PASSED 780s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 780s /usr/bin/bowtie2 --score-min L,7.50212977439213,6.89018979001145 --rfg 10.015147619549 --gbar 1 --trim3 5 --mp 7.30187690055908,5.82006667540673 --cp-ival 1 -D 17 --local -M 4 --trim5 6 --cp-min 3 --qseq -p 3 -x /tmp/Sim.pm.fu45He6P --reorder /tmp/Sim.pm.fu45He6P_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 780s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 780s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_107_107_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_107_107_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_110_110_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_110_110_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_116_116_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_116_116_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_118_118_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_131_131_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_131_131_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_132_132_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_132_132_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_133_133_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_143_143_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_143_143_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_145_145_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_145_145_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_159_159_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_159_159_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_160_160_1/1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_160_160_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_163_163_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_163_163_1/1' because it was < 2 characters long 780s Warning: skipping read 'R_1_1_1_165_165_1/1' because length (0) <= # seed mismatches (0) 780s Warning: skipping read 'R_1_1_1_165_165_1/1' because it was < 2 characters long 780s 168 reads; of these: 780s 168 (100.00%) were unpaired; of these: 780s 168 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.2 780s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.1 780s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 7 780s Reference gaps introduced: 1 780s Read gaps introduced: 0 780s Rearrangements introduced: 1 780s Created read sampler 780s Sampling 19 reads 780s Dumping reads to temporary files /tmp/Sim.pm.fu45He6P_1.raw & /tmp/Sim.pm.fu45He6P_2.raw 780s Parsing FASTA file /tmp/Sim.pm.fu45He6P.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 74 reference bases 780s *** Run 100 of 100 780s /usr/bin/bowtie2 --norc --cp-min 9 --mm -a --score-min L,3.28243787540459,2.26839767061817 --rfg 22.9830393765859,2.54688870463778 --rdg 8.37223678205168 --nofw --mp 7.64314371285365,3.31057087117737 -N 0 -L21 --local --cp-ival 2 -r -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw 780s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '2' because it was < 2 characters long 780s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '12' because it was < 2 characters long 780s 19 reads; of these: 780s 19 (100.00%) were paired; of these: 780s 19 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 19 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 19 pairs aligned 0 times concordantly or discordantly; of these: 780s 38 mates make up the pairs; of these: 780s 38 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 0 alignments, 0 edits 780s --------------- 780s PASSED 780s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 780s /usr/bin/bowtie2 --norc --cp-min 9 --mm -a --score-min L,3.28243787540459,2.26839767061817 --rfg 22.9830393765859,2.54688870463778 --rdg 8.37223678205168 --nofw --mp 7.64314371285365,3.31057087117737 -N 0 -L21 --local --cp-ival 2 -r -p 3 -x /tmp/Sim.pm.fu45He6P -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als 780s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '2' because it was < 2 characters long 780s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '12' because it was < 2 characters long 780s 19 reads; of these: 780s 19 (100.00%) were paired; of these: 780s 19 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 19 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 19 pairs aligned 0 times concordantly or discordantly; of these: 780s 38 mates make up the pairs; of these: 780s 38 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.px.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.als.sorted 780s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.fu45He6P.debug.als | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.debug.als.sorted 780s diff -uw /tmp/Sim.pm.fu45He6P.debug.als.sorted /tmp/Sim.pm.fu45He6P.px.als.sorted 780s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 780s /usr/bin/bowtie2 --norc --cp-min 9 --mm -a --score-min L,3.28243787540459,2.26839767061817 --rfg 22.9830393765859,2.54688870463778 --rdg 8.37223678205168 --nofw --mp 7.64314371285365,3.31057087117737 -N 0 -L21 --local --cp-ival 2 -r -p 2 -x /tmp/Sim.pm.fu45He6P --reorder -1 /tmp/Sim.pm.fu45He6P_1.raw -2 /tmp/Sim.pm.fu45He6P_2.raw | grep -v '^@PG' > /tmp/Sim.pm.fu45He6P.px.reord.als 780s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '2' because it was < 2 characters long 780s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '12' because it was < 2 characters long 780s 19 reads; of these: 780s 19 (100.00%) were paired; of these: 780s 19 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 19 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 19 pairs aligned 0 times concordantly or discordantly; of these: 780s 38 mates make up the pairs; of these: 780s 38 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s diff -uw /tmp/Sim.pm.fu45He6P.debug.als /tmp/Sim.pm.fu45He6P.px.reord.als 780s Created DNA generator 780s N frac: 0.026 780s IUPAC frac: 0.009 780s AT/ACGT frac: 0.547 780s A/AT frac: 0.610 780s C/CG frac: 0.700 780s Generating 2 references 780s Generated reference 'Sim.pm.1' of untrimmed length 71, trimmed length 33 780s Generated reference 'Sim.pm.2' of untrimmed length 115, trimmed length 53 780s Wrote references to /tmp/Sim.pm.GP7sSa1l.fa 780s A: 21 780s C: 29 780s G: 19 780s N: 1 780s T: 15 780s W: 1 780s *** TEST CASE *** 780s Executing: /usr/bin/bowtie2-build --dcv 2048 --bmaxdivn 1 --offrate 1 --threads 2 /tmp/Sim.pm.GP7sSa1l.fa /tmp/Sim.pm.GP7sSa1l 780s Settings: 780s Output files: "/tmp/Sim.pm.GP7sSa1l.*.bt2" 780s Line rate: 6 (line is 64 bytes) 780s Lines per side: 1 (side is 64 bytes) 780s Offset rate: 1 (one in 2) 780s FTable chars: 10 780s Strings: unpacked 780s Max bucket size: default 780s Max bucket size, sqrt multiplier: default 780s Max bucket size, len divisor: 1 780s Difference-cover sample period: 2048 780s Endianness: little 780s Actual local endianness: little 780s Sanity checking: disabled 780s Assertions: disabled 780s Random seed: 0 780s Sizeofs: void*:8, int:4, long:8, size_t:8 780s Input files DNA, FASTA: 780s /tmp/Sim.pm.GP7sSa1l.fa 780s Reading reference sizes 780s Time reading reference sizes: 00:00:00 780s Calculating joined length 780s Writing header 780s Reserving space for joined string 780s Joining reference sequences 780s Time to join reference sequences: 00:00:00 780s bmax according to bmaxDivN setting: 84 780s Using parameters --bmax 63 --dcv 2048 780s Doing ahead-of-time memory usage test 780s Building a SMALL index 780s Passed! Constructing with these parameters: --bmax 63 --dcv 2048 780s Constructing suffix-array element generator 780s Building DifferenceCoverSample 780s Building sPrime 780s Building sPrimeOrder 780s V-Sorting samples 780s V-Sorting samples time: 00:00:00 780s Allocating rank array 780s Ranking v-sort output 780s Ranking v-sort output time: 00:00:00 780s Invoking Larsson-Sadakane on ranks 780s Invoking Larsson-Sadakane on ranks time: 00:00:00 780s Sanity-checking and returning 780s Building samples 780s Reserving space for 4 sample suffixes 780s Generating random suffixes 780s QSorting 4 sample offsets, eliminating duplicates 780s QSorting sample offsets, eliminating duplicates time: 00:00:00 780s Multikey QSorting 4 samples 780s (Using difference cover) 780s Multikey QSorting samples time: 00:00:00 780s Calculating bucket sizes 780s Splitting and merging 780s Splitting and merging time: 00:00:00 780s Avg bucket size: 41.5 (target: 62) 780s Converting suffix-array elements to index image 780s Allocating ftab, absorbFtab 780s Entering Ebwt loop 780s Getting block 1 of 2 780s Reserving size (63) for bucket 1 780s Calculating Z arrays for bucket 1 780s Entering block accumulator loop for bucket 1: 780s bucket 1: 10% 780s bucket 1: 20% 780s bucket 1: 30% 780s bucket 1: 40% 780s bucket 1: 50% 780s bucket 1: 60% 780s bucket 1: 70% 780s bucket 1: 80% 780s bucket 1: 90% 780s bucket 1: 100% 780s Sorting block of length 41 for bucket 1 780s (Using difference cover) 780s Sorting block time: 00:00:00 780s Returning block of 42 for bucket 1 780s Getting block 2 of 2 780s Reserving size (63) for bucket 2 780s Calculating Z arrays for bucket 2 780s Entering block accumulator loop for bucket 2: 780s bucket 2: 10% 780s bucket 2: 20% 780s bucket 2: 30% 780s bucket 2: 40% 780s bucket 2: 50% 780s bucket 2: 60% 780s bucket 2: 70% 780s bucket 2: 80% 780s bucket 2: 90% 780s bucket 2: 100% 780s Sorting block of length 42 for bucket 2 780s (Using difference cover) 780s Sorting block time: 00:00:00 780s Returning block of 43 for bucket 2 780s Exited Ebwt loop 780s fchr[A]: 0 780s fchr[C]: 21 780s fchr[G]: 50 780s fchr[T]: 69 780s fchr[$]: 84 780s Exiting Ebwt::buildToDisk() 780s Returning from initFromVector 780s Wrote 4194587 bytes to primary EBWT file: /tmp/Sim.pm.GP7sSa1l.1.bt2.tmp 780s Wrote 176 bytes to secondary EBWT file: /tmp/Sim.pm.GP7sSa1l.2.bt2.tmp 780s Re-opening _in1 and _in2 as input streams 780s Returning from Ebwt constructor 780s Headers: 780s len: 84 780s bwtLen: 85 780s sz: 21 780s bwtSz: 22 780s lineRate: 6 780s offRate: 1 780s offMask: 0xfffffffe 780s ftabChars: 10 780s eftabLen: 20 780s eftabSz: 80 780s ftabLen: 1048577 780s ftabSz: 4194308 780s offsLen: 43 780s offsSz: 172 780s lineSz: 64 780s sideSz: 64 780s sideBwtSz: 48 780s sideBwtLen: 192 780s numSides: 1 780s numLines: 1 780s ebwtTotLen: 64 780s ebwtTotSz: 64 780s color: 0 780s reverse: 0 780s Total time for call to driver() for forward index: 00:00:00 780s Reading reference sizes 780s Time reading reference sizes: 00:00:00 780s Calculating joined length 780s Writing header 780s Reserving space for joined string 780s Joining reference sequences 780s Time to join reference sequences: 00:00:00 780s Time to reverse reference sequence: 00:00:00 780s bmax according to bmaxDivN setting: 84 780s Using parameters --bmax 63 --dcv 2048 780s Doing ahead-of-time memory usage test 780s Passed! Constructing with these parameters: --bmax 63 --dcv 2048 780s Constructing suffix-array element generator 780s Building DifferenceCoverSample 780s Building sPrime 780s Building sPrimeOrder 780s V-Sorting samples 780s V-Sorting samples time: 00:00:00 780s Allocating rank array 780s Ranking v-sort output 780s Ranking v-sort output time: 00:00:00 780s Invoking Larsson-Sadakane on ranks 780s Invoking Larsson-Sadakane on ranks time: 00:00:00 780s Sanity-checking and returning 780s Building samples 780s Reserving space for 4 sample suffixes 780s Generating random suffixes 780s QSorting 4 sample offsets, eliminating duplicates 780s QSorting sample offsets, eliminating duplicates time: 00:00:00 780s Multikey QSorting 4 samples 780s (Using difference cover) 780s Multikey QSorting samples time: 00:00:00 780s Calculating bucket sizes 780s Splitting and merging 780s Splitting and merging time: 00:00:00 780s Avg bucket size: 41.5 (target: 62) 780s Converting suffix-array elements to index image 780s Allocating ftab, absorbFtab 780s Entering Ebwt loop 780s Getting block 1 of 2 780s Reserving size (63) for bucket 1 780s Calculating Z arrays for bucket 1 780s Entering block accumulator loop for bucket 1: 780s bucket 1: 10% 780s bucket 1: 20% 780s bucket 1: 30% 780s bucket 1: 40% 780s bucket 1: 50% 780s bucket 1: 60% 780s bucket 1: 70% 780s bucket 1: 80% 780s bucket 1: 90% 780s bucket 1: 100% 780s Sorting block of length 53 for bucket 1 780s (Using difference cover) 780s Sorting block time: 00:00:00 780s Returning block of 54 for bucket 1 780s Getting block 2 of 2 780s Reserving size (63) for bucket 2 780s Calculating Z arrays for bucket 2 780s Entering block accumulator loop for bucket 2: 780s bucket 2: 10% 780s bucket 2: 20% 780s bucket 2: 30% 780s bucket 2: 40% 780s bucket 2: 50% 780s bucket 2: 60% 780s bucket 2: 70% 780s bucket 2: 80% 780s bucket 2: 90% 780s bucket 2: 100% 780s Sorting block of length 30 for bucket 2 780s (Using difference cover) 780s Sorting block time: 00:00:00 780s Returning block of 31 for bucket 2 780s Exited Ebwt loop 780s fchr[A]: 0 780s fchr[C]: 21 780s fchr[G]: 50 780s fchr[T]: 69 780s fchr[$]: 84 780s Exiting Ebwt::buildToDisk() 780s Returning from initFromVector 780s Wrote 4194587 bytes to primary EBWT file: /tmp/Sim.pm.GP7sSa1l.rev.1.bt2.tmp 780s Wrote 176 bytes to secondary EBWT file: /tmp/Sim.pm.GP7sSa1l.rev.2.bt2.tmp 780s Re-opening _in1 and _in2 as input streams 780s Returning from Ebwt constructor 780s Headers: 780s len: 84 780s bwtLen: 85 780s sz: 21 780s bwtSz: 22 780s lineRate: 6 780s offRate: 1 780s offMask: 0xfffffffe 780s ftabChars: 10 780s eftabLen: 20 780s eftabSz: 80 780s ftabLen: 1048577 780s ftabSz: 4194308 780s offsLen: 43 780s offsSz: 172 780s lineSz: 64 780s sideSz: 64 780s sideBwtSz: 48 780s sideBwtLen: 192 780s numSides: 1 780s numLines: 1 780s ebwtTotLen: 64 780s ebwtTotSz: 64 780s color: 0 780s reverse: 1 780s Total time for backward call to driver() for mirror index: 00:00:00 780s Renaming /tmp/Sim.pm.GP7sSa1l.3.bt2.tmp to /tmp/Sim.pm.GP7sSa1l.3.bt2 780s Renaming /tmp/Sim.pm.GP7sSa1l.4.bt2.tmp to /tmp/Sim.pm.GP7sSa1l.4.bt2 780s Renaming /tmp/Sim.pm.GP7sSa1l.1.bt2.tmp to /tmp/Sim.pm.GP7sSa1l.1.bt2 780s Renaming /tmp/Sim.pm.GP7sSa1l.2.bt2.tmp to /tmp/Sim.pm.GP7sSa1l.2.bt2 780s Renaming /tmp/Sim.pm.GP7sSa1l.rev.1.bt2.tmp to /tmp/Sim.pm.GP7sSa1l.rev.1.bt2 780s Renaming /tmp/Sim.pm.GP7sSa1l.rev.2.bt2.tmp to /tmp/Sim.pm.GP7sSa1l.rev.2.bt2 780s Built nucleotide index '/tmp/Sim.pm.GP7sSa1l' 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.1 780s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.2 780s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 6 780s Reference gaps introduced: 0 780s Read gaps introduced: 1 780s Rearrangements introduced: 0 780s Created read sampler 780s Sampling 26 reads 780s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 780s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 86 reference bases 780s *** Run 1 of 100 780s /usr/bin/bowtie2 --cp-min 2 -i L,0.310290359600764 --mp 5.14188429390088,3.34054016598776 --cp-ival 1 --local --mm -a --rdg 48.1682007370037 --score-min L,7.60865073825015,9.72013187977076 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 780s 26 reads; of these: 780s 26 (100.00%) were unpaired; of these: 780s 26 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 0 alignments, 0 edits 780s --------------- 780s PASSED 780s ALSO checking that bowtie2 and bowtie2-align match up 780s /usr/bin/bowtie2 --cp-min 2 -i L,0.310290359600764 --mp 5.14188429390088,3.34054016598776 --cp-ival 1 --local --mm -a --rdg 48.1682007370037 --score-min L,7.60865073825015,9.72013187977076 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 780s 26 reads; of these: 780s 26 (100.00%) were unpaired; of these: 780s 26 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.1 780s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.2 780s Introducing 11 SNPs, 1/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 14 780s Reference gaps introduced: 1 780s Read gaps introduced: 0 780s Rearrangements introduced: 0 780s Created read sampler 780s Sampling 68 reads 780s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 780s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 86 reference bases 780s *** Run 2 of 100 780s /usr/bin/bowtie2 --trim5 9 --mm --score-min L,2.17499170772466,9.34291587963135 --gbar 2 -R 1 -N 1 -L29 --mp 8.06646157365723,1.42359017627554 --local --cp-ival 1 --cp-min 6 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 780s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '6' because it was < 2 characters long 780s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '9' because it was < 2 characters long 780s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '15' because it was < 2 characters long 780s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '16' because it was < 2 characters long 780s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '21' because it was < 2 characters long 780s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '23' because it was < 2 characters long 780s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '25' because it was < 2 characters long 780s Warning: skipping read '29' because length (1) <= # seed mismatches (1) 780s Warning: skipping read '29' because it was < 2 characters long 780s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '31' because it was < 2 characters long 780s Warning: skipping read '34' because length (1) <= # seed mismatches (1) 780s Warning: skipping read '34' because it was < 2 characters long 780s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '35' because it was < 2 characters long 780s Warning: skipping read '42' because length (1) <= # seed mismatches (1) 780s Warning: skipping read '42' because it was < 2 characters long 780s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '43' because it was < 2 characters long 780s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '44' because it was < 2 characters long 780s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '45' because it was < 2 characters long 780s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '48' because it was < 2 characters long 780s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '49' because it was < 2 characters long 780s Warning: skipping read '50' because length (1) <= # seed mismatches (1) 780s Warning: skipping read '50' because it was < 2 characters long 780s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '51' because it was < 2 characters long 780s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '56' because it was < 2 characters long 780s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '58' because it was < 2 characters long 780s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '59' because it was < 2 characters long 780s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '63' because it was < 2 characters long 780s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '67' because it was < 2 characters long 780s 68 reads; of these: 780s 68 (100.00%) were unpaired; of these: 780s 68 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s Read 50 alignments... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 0 alignments, 0 edits 780s --------------- 780s PASSED 780s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 780s /usr/bin/bowtie2 --trim5 9 --mm --score-min L,2.17499170772466,9.34291587963135 --gbar 2 -R 1 -N 1 -L29 --mp 8.06646157365723,1.42359017627554 --local --cp-ival 1 --cp-min 6 -f -p 2 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 780s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '6' because it was < 2 characters long 780s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '9' because it was < 2 characters long 780s Warning: skipping read '15' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '15' because it was < 2 characters long 780s Warning: skipping read '16' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '16' because it was < 2 characters long 780s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '21' because it was < 2 characters long 780s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '23' because it was < 2 characters long 780s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '25' because it was < 2 characters long 780s Warning: skipping read '29' because length (1) <= # seed mismatches (1) 780s Warning: skipping read '29' because it was < 2 characters long 780s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '31' because it was < 2 characters long 780s Warning: skipping read '34' because length (1) <= # seed mismatches (1) 780s Warning: skipping read '34' because it was < 2 characters long 780s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '35' because it was < 2 characters long 780s Warning: skipping read '42' because length (1) <= # seed mismatches (1) 780s Warning: skipping read '42' because it was < 2 characters long 780s Warning: skipping read '43' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '43' because it was < 2 characters long 780s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '44' because it was < 2 characters long 780s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '45' because it was < 2 characters long 780s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '48' because it was < 2 characters long 780s Warning: skipping read '49' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '49' because it was < 2 characters long 780s Warning: skipping read '50' because length (1) <= # seed mismatches (1) 780s Warning: skipping read '50' because it was < 2 characters long 780s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '51' because it was < 2 characters long 780s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '56' because it was < 2 characters long 780s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '58' because it was < 2 characters long 780s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '59' because it was < 2 characters long 780s Warning: skipping read '63' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '63' because it was < 2 characters long 780s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 780s Warning: skipping read '67' because it was < 2 characters long 780s 68 reads; of these: 780s 68 (100.00%) were unpaired; of these: 780s 68 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 780s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 780s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.1 780s Introducing 0 SNPs, 2/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.2 780s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 6 780s Reference gaps introduced: 2 780s Read gaps introduced: 0 780s Rearrangements introduced: 2 780s Created read sampler 780s Sampling 25 reads 780s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 780s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 86 reference bases 780s *** Run 3 of 100 780s /usr/bin/bowtie2 --cp-min 3 --norc -k 15 --trim5 8 --cp-ival 1 --mp 8.38836274808777,1.90927347693976 --trim3 5 --gbar 1 --rfg 35.8799969813785 --rdg 9.89712242980274 --score-min L,7.61734174539989,2.90202004680024 --mm -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 780s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 780s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read '1' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 780s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '2' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 780s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '3' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 780s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '7' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 780s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '10' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 780s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '14' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 780s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '15' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 780s 25 reads; of these: 780s 16 (64.00%) were paired; of these: 780s 16 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 16 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 16 pairs aligned 0 times concordantly or discordantly; of these: 780s 32 mates make up the pairs; of these: 780s 31 (96.88%) aligned 0 times 780s 1 (3.12%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 9 (36.00%) were unpaired; of these: 780s 9 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 2.44% overall alignment rate 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GATCTCAA 780s GATCTCAA 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 1 alignments, 0 edits 780s --------------- 780s PASSED 780s ALSO checking that bowtie2 and bowtie2-align match up 780s /usr/bin/bowtie2 --cp-min 3 --norc -k 15 --trim5 8 --cp-ival 1 --mp 8.38836274808777,1.90927347693976 --trim3 5 --gbar 1 --rfg 35.8799969813785 --rdg 9.89712242980274 --score-min L,7.61734174539989,2.90202004680024 --mm -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 780s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 780s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read '1' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 780s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '2' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 780s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '3' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 780s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '7' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 780s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '10' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 780s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '14' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 780s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '15' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 780s 25 reads; of these: 780s 16 (64.00%) were paired; of these: 780s 16 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 16 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 16 pairs aligned 0 times concordantly or discordantly; of these: 780s 32 mates make up the pairs; of these: 780s 31 (96.88%) aligned 0 times 780s 1 (3.12%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 9 (36.00%) were unpaired; of these: 780s 9 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 2.44% overall alignment rate 780s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 780s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 780s /usr/bin/bowtie2 --cp-min 3 --norc -k 15 --trim5 8 --cp-ival 1 --mp 8.38836274808777,1.90927347693976 --trim3 5 --gbar 1 --rfg 35.8799969813785 --rdg 9.89712242980274 --score-min L,7.61734174539989,2.90202004680024 --mm -q -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 780s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 780s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 780s Warning: skipping read '1' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 780s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '2' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 780s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '3' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 780s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '7' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 780s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '10' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 780s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '14' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 780s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '15' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 780s 25 reads; of these: 780s 16 (64.00%) were paired; of these: 780s 16 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 16 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 16 pairs aligned 0 times concordantly or discordantly; of these: 780s 32 mates make up the pairs; of these: 780s 31 (96.88%) aligned 0 times 780s 1 (3.12%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 9 (36.00%) were unpaired; of these: 780s 9 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 2.44% overall alignment rate 780s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.2 780s Introducing 5 SNPs, 0/0 ref/read gaps, and 2 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.1 780s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 6 780s Reference gaps introduced: 0 780s Read gaps introduced: 0 780s Rearrangements introduced: 2 780s Created read sampler 780s Sampling 90 reads 780s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 780s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 86 reference bases 780s *** Run 4 of 100 780s /usr/bin/bowtie2 --score-min L,5.98892157155012,8.49300266611633 --mm -D 13 --local --cp-ival 2 --cp-min 3 --mp 7.86836403925482,2.25830858710978 --trim3 1 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 780s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 780s Warning: skipping read '49' because it was < 2 characters long 780s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '74' because it was < 2 characters long 780s Warning: skipping read '84' because length (1) <= # seed mismatches (0) 780s Warning: skipping read '84' because it was < 2 characters long 780s 90 reads; of these: 780s 90 (100.00%) were unpaired; of these: 780s 90 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 0.00% overall alignment rate 780s Read 50 alignments... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 0 alignments, 0 edits 780s --------------- 780s PASSED 780s Flattened IUPAC characters 780s Mutating sequence Sim.pm.1 780s Introducing 3 SNPs, 1/0 ref/read gaps, and 2 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutating sequence Sim.pm.2 780s Introducing 2 SNPs, 3/0 ref/read gaps, and 1 rearrangements 780s Finished SNPs 780s Finished ref gaps 780s Finished read gaps 780s Mutated reference genome to subject genome 780s SNPs introduced: 5 780s Reference gaps introduced: 4 780s Read gaps introduced: 0 780s Rearrangements introduced: 3 780s Created read sampler 780s Sampling 121 reads 780s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 780s *** Run 5 of 100 780s /usr/bin/bowtie2 --cp-ival 1 --nofw --mp 9.59338225211832,1.07464900209809 --trim3 5 --score-min L,4.99104405298771,9.38847447141089 --rfg 7.34274736751501,14.0402746202533 --mm --cp-min 2 -R 2 --np 1 -k 4 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 780s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 780s parsing sequence Sim.pm.1... 780s parsing sequence Sim.pm.2... 780s Parsed 86 reference bases 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 780s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '3' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 780s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '5' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 780s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '14' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 780s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '21' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 780s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '25' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 780s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '34' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 780s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '37' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 780s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '42' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 780s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '51' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 780s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '54' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 780s Read 50 alignments... 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 780s Read 100 alignments... 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 780s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 780s Warning: skipping mate #2 of read '71' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 780s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 780s Warning: skipping read '87' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 780s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '93' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 780s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '94' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 780s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '96' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 780s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '97' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 780s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 780s Warning: skipping mate #1 of read '117' because it was < 2 characters long 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 780s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 780s 121 reads; of these: 780s 108 (89.26%) were paired; of these: 780s 108 (100.00%) aligned concordantly 0 times 780s 0 (0.00%) aligned concordantly exactly 1 time 780s 0 (0.00%) aligned concordantly >1 times 780s ---- 780s 108 pairs aligned concordantly 0 times; of these: 780s 0 (0.00%) aligned discordantly 1 time 780s ---- 780s 108 pairs aligned 0 times concordantly or discordantly; of these: 780s 216 mates make up the pairs; of these: 780s 186 (86.11%) aligned 0 times 780s 20 (9.26%) aligned exactly 1 time 780s 10 (4.63%) aligned >1 times 780s 13 (10.74%) were unpaired; of these: 780s 13 (100.00%) aligned 0 times 780s 0 (0.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 13.10% overall alignment rate 780s Read 150 alignments... 780s Read 200 alignments... 780s Read 250 alignments... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s ATTC 780s ATTC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s ATC 780s ATC 780s Processing line... 780s ATC 780s ATC 780s Processing line... 780s ATC 780s ATC 780s Processing line... 780s Processing line... 780s TCGAAT 780s TCGAAT 780s Processing line... 780s Processing line... 780s TTT 780s TTT 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s TCGAATCATGACTGGATCTCAA 780s TCGAATCATGACTGGATCTCAA 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s ATTCGAAT 780s ATTCGAAT 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GA 780s GA 780s Processing line... 780s GA 780s GA 780s Processing line... 780s GA 780s GA 780s Processing line... 780s GA 780s GA 780s Processing line... 780s Processing line... 780s TG 780s TG 780s Processing line... 780s TG 780s TG 780s Processing line... 780s TG 780s TG 780s Processing line... 780s TG 780s TG 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GGATCT 780s GGATCT 780s Processing line... 780s Processing line... 780s TCGAAT 780s TCGAAT 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GA 780s GA 780s Processing line... 780s GA 780s GA 780s Processing line... 780s GA 780s GA 780s Processing line... 780s GA 780s GA 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s AATCATGA 780s AATCATGA 780s Processing line... 780s Processing line... 780s Processing line... 780s AC 780s AC 780s Processing line... 780s AC 780s AC 780s Processing line... 780s AC 780s AC 780s Processing line... 780s AC 780s AC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s AA 780s AA 780s Processing line... 780s AA 780s AA 780s Processing line... 780s AA 780s AA 780s Processing line... 780s AA 780s AA 780s Processing line... 780s Processing line... 780s ATTCGAATCATGACTGGATCT 780s ATTCGAATCATGACTGGATCT 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GGATCTCAAA 780s GGATCTCAAA 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GATCTCAAAT 780s GATCTCAAAT 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s ATTCG 780s ATTCG 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s TGA 780s TGA 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s ACTGGATCTC 780s ACTGGATCTC 780s Processing line... 780s Processing line... 780s Processing line... 780s CAA 780s CAA 780s Processing line... 780s CAA 780s CAA 780s Processing line... 780s CAA 780s CAA 780s Processing line... 780s CAA 780s CAA 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GACTGGATC 780s GACTGGATC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s GACTGGATC 780s GACTGGATC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s TGC 780s TGC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s CAATTCGAATCATGACTGGATCTC 780s CAATTCGAATCATGACTGGATCTC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s AA 780s AA 780s Processing line... 780s AA 780s AA 780s Processing line... 780s AA 780s AA 780s Processing line... 780s AA 780s AA 780s Processing line... 780s Processing line... 780s GAATCATGACTGGATC 780s GAATCATGACTGGATC 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s Processing line... 780s AG 780s AG 780s Processing line... 780s AG 780s AG 780s Processing line... 780s Processing line... 780s AATTCGAA 780s AATTCGAA 780s Processing line... 780s Processing line... 780s CG 780s CG 780s Processing line... 780s CG 780s CG 780s Processing line... 780s CG 780s CG 780s Processing line... 780s CG 780s CG 780s Processing line... 780s Processing line... 780s Processing line... 780s --- Summary --- 780s Read 1 reference strings 780s Checked 57 alignments, 0 edits 780s --------------- 780s PASSED 780s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 780s /usr/bin/bowtie2 --cp-ival 1 --nofw --mp 9.59338225211832,1.07464900209809 --trim3 5 --score-min L,4.99104405298771,9.38847447141089 --rfg 7.34274736751501,14.0402746202533 --mm --cp-min 2 -R 2 --np 1 -k 4 -q -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 781s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '3' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 781s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '5' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 781s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '14' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 781s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '21' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 781s Warning: skipping mate #1 of read '25' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '25' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 781s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '34' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 781s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '37' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 781s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '42' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 781s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '51' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 781s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #2 of read '54' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 781s Warning: skipping mate #2 of read '71' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #2 of read '71' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 781s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '87' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 781s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '93' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 781s Warning: skipping mate #1 of read '94' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '94' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 781s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '96' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 781s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '97' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 781s Warning: skipping mate #1 of read '117' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '117' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 781s 121 reads; of these: 781s 108 (89.26%) were paired; of these: 781s 108 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 108 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 108 pairs aligned 0 times concordantly or discordantly; of these: 781s 216 mates make up the pairs; of these: 781s 186 (86.11%) aligned 0 times 781s 20 (9.26%) aligned exactly 1 time 781s 10 (4.63%) aligned >1 times 781s 13 (10.74%) were unpaired; of these: 781s 13 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 13.10% overall alignment rate 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.2 781s Introducing 7 SNPs, 1/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.1 781s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s SNPs introduced: 9 781s Reference gaps introduced: 1 781s Read gaps introduced: 0 781s Rearrangements introduced: 1 781s Created read sampler 781s Sampling 71 reads 781s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 781s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 86 reference bases 781s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 781s *** Run 6 of 100 781s /usr/bin/bowtie2 --mp 4.40249395892582,2.6261083987631 --local --cp-ival 1 --cp-min 14 --trim5 5 --score-min L,6.35685846504428,5.48263700633503 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 781s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '3' because it was < 2 characters long 781s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '9' because it was < 2 characters long 781s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '15' because it was < 2 characters long 781s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '35' because it was < 2 characters long 781s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '44' because it was < 2 characters long 781s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '57' because it was < 2 characters long 781s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '59' because it was < 2 characters long 781s Read 50 alignments... 781s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '70' because it was < 2 characters long 781s Read 100 alignments... 781s 71 reads; of these: 781s 63 (88.73%) were paired; of these: 781s 63 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 63 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 63 pairs aligned 0 times concordantly or discordantly; of these: 781s 126 mates make up the pairs; of these: 781s 126 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 8 (11.27%) were unpaired; of these: 781s 8 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 0 alignments, 0 edits 781s --------------- 781s PASSED 781s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 781s /usr/bin/bowtie2 --mp 4.40249395892582,2.6261083987631 --local --cp-ival 1 --cp-min 14 --trim5 5 --score-min L,6.35685846504428,5.48263700633503 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 781s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '3' because it was < 2 characters long 781s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '9' because it was < 2 characters long 781s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '15' because it was < 2 characters long 781s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '35' because it was < 2 characters long 781s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '44' because it was < 2 characters long 781s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '57' because it was < 2 characters long 781s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '59' because it was < 2 characters long 781s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read '70' because it was < 2 characters long 781s 71 reads; of these: 781s 63 (88.73%) were paired; of these: 781s 63 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 63 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 63 pairs aligned 0 times concordantly or discordantly; of these: 781s 126 mates make up the pairs; of these: 781s 126 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 8 (11.27%) were unpaired; of these: 781s 8 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.2 781s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.1 781s Introducing 9 SNPs, 0/0 ref/read gaps, and 4 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 781s SNPs introduced: 9 781s Reference gaps introduced: 1 781s Read gaps introduced: 0 781s Rearrangements introduced: 4 781s Created read sampler 781s Sampling 120 reads 781s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 781s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 86 reference bases 781s *** Run 7 of 100 781s /usr/bin/bowtie2 --trim5 1 -M 4 --np 1 --cp-min 3 --rfg 3.29459588324681 --score-min L,2.77087908122908,6.59357235927771 --gbar 1 --trim3 2 -N 0 --cp-ival 1 --n-ceil 0.055705207276597,0.504824879770221 --local --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 781s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 781s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 781s Read 50 alignments... 781s Read 100 alignments... 781s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 781s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 781s Read 150 alignments... 781s 120 reads; of these: 781s 110 (91.67%) were paired; of these: 781s 110 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 110 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 110 pairs aligned 0 times concordantly or discordantly; of these: 781s 220 mates make up the pairs; of these: 781s 220 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 10 (8.33%) were unpaired; of these: 781s 10 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s Read 200 alignments... 781s Processing line... 781s Processing line... 781s Processing line... 781s /usr/bin/bowtie2 --trim5 1 -M 4 --np 1 --cp-min 3 --rfg 3.29459588324681 --score-min L,2.77087908122908,6.59357235927771 --gbar 1 --trim3 2 -N 0 --cp-ival 1 --n-ceil 0.055705207276597,0.504824879770221 --local --qseq -p 2 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 0 alignments, 0 edits 781s --------------- 781s PASSED 781s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 781s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 781s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 781s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #2 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 781s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #2 of read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_113_113_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 781s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 781s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 781s 120 reads; of these: 781s 110 (91.67%) were paired; of these: 781s 110 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 110 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 110 pairs aligned 0 times concordantly or discordantly; of these: 781s 220 mates make up the pairs; of these: 781s 220 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 10 (8.33%) were unpaired; of these: 781s 10 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 781s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 781s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.2 781s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.1 781s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s SNPs introduced: 3 781s Reference gaps introduced: 0 781s Read gaps introduced: 0 781s Rearrangements introduced: 1 781s Created read sampler 781s Sampling 115 reads 781s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 781s *** Run 8 of 100 781s /usr/bin/bowtie2 --trim3 3 --cp-ival 1 --local --nofw -N 1 -L25 --mp 4.48446047174704,2.61245039713489 --mm --score-min L,4.51383384674596,3.7821663671565 --rdg 5.90462220594887 --cp-min 2 -i L,0.47092653812317 -M 2 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 781s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 86 reference bases 781s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 781s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '8' because it was < 2 characters long 781s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (1) 781s Warning: skipping mate #2 of read '13' because it was < 2 characters long 781s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '16' because it was < 2 characters long 781s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '33' because it was < 2 characters long 781s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '36' because it was < 2 characters long 781s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '68' because it was < 2 characters long 781s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '77' because it was < 2 characters long 781s Warning: skipping read '78' because length (1) <= # seed mismatches (1) 781s Warning: skipping read '78' because it was < 2 characters long 781s Read 50 alignments... 781s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '83' because it was < 2 characters long 781s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '96' because it was < 2 characters long 781s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '98' because it was < 2 characters long 781s Warning: skipping read '114' because length (0) <= # seed mismatches (1) 781s Warning: skipping read '114' because it was < 2 characters long 781s Read 100 alignments... 781s 115 reads; of these: 781s 108 (93.91%) were paired; of these: 781s 108 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 108 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 108 pairs aligned 0 times concordantly or discordantly; of these: 781s 216 mates make up the pairs; of these: 781s 216 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 7 (6.09%) were unpaired; of these: 781s 7 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s Read 150 alignments... 781s Read 200 alignments... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s /usr/bin/bowtie2 --trim3 3 --cp-ival 1 --local --nofw -N 1 -L25 --mp 4.48446047174704,2.61245039713489 --mm --score-min L,4.51383384674596,3.7821663671565 --rdg 5.90462220594887 --cp-min 2 -i L,0.47092653812317 -M 2 -q -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 0 alignments, 0 edits 781s --------------- 781s PASSED 781s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 781s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 781s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '8' because it was < 2 characters long 781s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (1) 781s Warning: skipping mate #2 of read '13' because it was < 2 characters long 781s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '16' because it was < 2 characters long 781s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '33' because it was < 2 characters long 781s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '36' because it was < 2 characters long 781s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '68' because it was < 2 characters long 781s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '77' because it was < 2 characters long 781s Warning: skipping read '78' because length (1) <= # seed mismatches (1) 781s Warning: skipping read '78' because it was < 2 characters long 781s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '83' because it was < 2 characters long 781s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '96' because it was < 2 characters long 781s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '98' because it was < 2 characters long 781s Warning: skipping read '114' because length (0) <= # seed mismatches (1) 781s Warning: skipping read '114' because it was < 2 characters long 781s 115 reads; of these: 781s 108 (93.91%) were paired; of these: 781s 108 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 108 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 108 pairs aligned 0 times concordantly or discordantly; of these: 781s 216 mates make up the pairs; of these: 781s 216 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 7 (6.09%) were unpaired; of these: 781s 7 (100.00%) aligned 0 times 781s 0 (0.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 0.00% overall alignment rate 781s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.1 781s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.2 781s Introducing 6 SNPs, 2/1 ref/read gaps, and 1 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s SNPs introduced: 11 781s Reference gaps introduced: 2 781s Read gaps introduced: 1 781s Rearrangements introduced: 1 781s Created read sampler 781s Sampling 83 reads 781s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 781s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 86 reference bases 781s *** Run 9 of 100 781s /usr/bin/bowtie2 --score-min L,4.06142819077773,3.67942830303284 --np 2 --gbar 4 -k 5 --nofw -N 0 -L31 --cp-min 6 --cp-ival 1 --n-ceil 0.0134426363011003,1.19311601012706 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 781s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #2 of read '57' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 781s Read 50 alignments... 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 781s Read 100 alignments... 781s 83 reads; of these: 781s 83 (100.00%) were paired; of these: 781s 83 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 83 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 83 pairs aligned 0 times concordantly or discordantly; of these: 781s 166 mates make up the pairs; of these: 781s 149 (89.76%) aligned 0 times 781s 15 (9.04%) aligned exactly 1 time 781s 2 (1.20%) aligned >1 times 781s 10.24% overall alignment rate 781s Read 150 alignments... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GAGGCAC 781s GAGGCAC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GGAGG 781s GGAGG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s AATCA 781s AATCA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CGGGAGGCAC 781s CGGGAGGCAC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s ATCATGACTGGAT 781s ATCATGACTGGAT 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CGAATCATGACTGGATCTCA 781s CGAATCATGACTGGATCTCA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TGACTGGAT 781s TGACTGGAT 781s Processing line... 781s Processing line... 781s ATTCG 781s ATTCG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GGAGG 781s GGAGG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TCTCAAAT 781s TCTCAAAT 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CGGGAGGC 781s CGGGAGGC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TCGAATCATGACTGGATCTCAA 781s TCGAATCATGACTGGATCTCAA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GG 781s GG 781s Processing line... 781s GG 781s GG 781s Processing line... 781s GG 781s GG 781s Processing line... 781s GG 781s GG 781s Processing line... 781s GG 781s GG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CAATTCGAATCATGACTGGAT 781s CAATTCGAATCATGACTGGAT 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GAATCATGACTGGATCTCAAAT 781s GAATCATGACTGGATCTCAAAT 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GGAG 781s GGAG 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 25 alignments, 0 edits 781s --------------- 781s PASSED 781s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 781s /usr/bin/bowtie2 --score-min L,4.06142819077773,3.67942830303284 --np 2 --gbar 4 -k 5 --nofw -N 0 -L31 --cp-min 6 --cp-ival 1 --n-ceil 0.0134426363011003,1.19311601012706 -q -p 2 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 781s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 781s Warning: skipping mate #2 of read '57' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 781s 83 reads; of these: 781s 83 (100.00%) were paired; of these: 781s 83 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 83 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 83 pairs aligned 0 times concordantly or discordantly; of these: 781s 166 mates make up the pairs; of these: 781s 149 (89.76%) aligned 0 times 781s 15 (9.04%) aligned exactly 1 time 781s 2 (1.20%) aligned >1 times 781s 10.24% overall alignment rate 781s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 781s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 781s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.1 781s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.2 781s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s SNPs introduced: 4 781s Reference gaps introduced: 0 781s Read gaps introduced: 1 781s Rearrangements introduced: 0 781s Created read sampler 781s Sampling 84 reads 781s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 781s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 86 reference bases 781s *** Run 10 of 100 781s /usr/bin/bowtie2 -D 40 --cp-ival 2 --trim3 9 --gbar 6 --rfg 13.206144932435 --score-min L,9.03493458264016,6.08496520632042 --cp-min 6 --np 2 -k 5 --trim5 0 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 781s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 781s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '1' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 781s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '8' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 781s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '10' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 781s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '16' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 781s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '19' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 781s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '22' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 781s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '25' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 781s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '27' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 781s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '29' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 781s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '30' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 781s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '31' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 781s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '37' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 781s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '39' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 781s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 781s Warning: skipping read '45' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 781s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '46' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 781s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '48' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 781s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '50' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 781s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '52' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 781s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '54' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 781s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '57' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 781s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '58' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 781s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '61' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 781s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '63' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 781s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '69' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 781s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '71' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 781s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '72' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 781s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '73' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 781s 84 reads; of these: 781s 84 (100.00%) were unpaired; of these: 781s 74 (88.10%) aligned 0 times 781s 7 (8.33%) aligned exactly 1 time 781s 3 (3.57%) aligned >1 times 781s 11.90% overall alignment rate 781s Read 50 alignments... 781s Read 100 alignments... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TT 781s TT 781s Processing line... 781s TT 781s TT 781s Processing line... 781s TT 781s TT 781s Processing line... 781s AA 781s AA 781s Processing line... 781s AA 781s AA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s AACGGCCGCCACCCTCTTTCC 781s AACGGCCGCCACCCTCTTTCC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GTGCAATT 781s GTGCAATT 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s ACGGCCGCCACC 781s ACGGCCGCCACC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s AATCATGACTGGA 781s AATCATGACTGGA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CCACCCTCTTTCCC 781s CCACCCTCTTTCCC 781s Processing line... 781s TGTGCAATTC 781s TGTGCAATTC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GG 781s GG 781s Processing line... 781s GG 781s GG 781s Processing line... 781s GG 781s GG 781s Processing line... 781s GG 781s GG 781s Processing line... 781s GG 781s GG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s ATTCGAATCATGAC 781s ATTCGAATCATGAC 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 22 alignments, 0 edits 781s --------------- 781s PASSED 781s ALSO checking that bowtie2 and bowtie2-align match up 781s /usr/bin/bowtie2 -D 40 --cp-ival 2 --trim3 9 --gbar 6 --rfg 13.206144932435 --score-min L,9.03493458264016,6.08496520632042 --cp-min 6 --np 2 -k 5 --trim5 0 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 781s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 781s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '1' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 781s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '8' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 781s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '10' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 781s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '16' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 781s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '19' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 781s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '22' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 781s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '25' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 781s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '27' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 781s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '29' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 781s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '30' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 781s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '31' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 781s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '37' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 781s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '39' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 781s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 781s Warning: skipping read '45' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 781s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '46' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 781s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '48' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 781s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '50' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 781s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '52' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 781s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '54' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 781s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '57' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 781s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '58' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 781s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '61' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 781s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '63' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 781s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '69' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 781s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '71' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 781s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '72' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 781s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 781s Warning: skipping read '73' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 781s 84 reads; of these: 781s 84 (100.00%) were unpaired; of these: 781s 74 (88.10%) aligned 0 times 781s 7 (8.33%) aligned exactly 1 time 781s 3 (3.57%) aligned >1 times 781s 11.90% overall alignment rate 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.1 781s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.2 781s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 781s SNPs introduced: 6 781s Reference gaps introduced: 0 781s Read gaps introduced: 1 781s Rearrangements introduced: 0 781s Created read sampler 781s Sampling 20 reads 781s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 781s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 86 reference bases 781s *** Run 11 of 100 781s /usr/bin/bowtie2 --rfg 29.8689578752319,15.3204355497086 --rdg 30.5639233607489,1.10058483227608 --score-min L,1.67949807213495,5.25701611295639 -k 4 --cp-ival 2 -D 15 --cp-min 9 -R 1 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 781s 20 reads; of these: 781s 20 (100.00%) were paired; of these: 781s 20 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 20 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 20 pairs aligned 0 times concordantly or discordantly; of these: 781s 40 mates make up the pairs; of these: 781s 33 (82.50%) aligned 0 times 781s 5 (12.50%) aligned exactly 1 time 781s 2 (5.00%) aligned >1 times 781s 17.50% overall alignment rate 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CACCGGGAGGC 781s CACCGGGAGGC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TTCGAATCATGACTGGATC 781s TTCGAATCATGACTGGATC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CACCGGGAGGCA 781s CACCGGGAGGCA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TGGATCTCA 781s TGGATCTCA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s AATCATGACTGGATCTCAAA 781s AATCATGACTGGATCTCAAA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CAC 781s CAC 781s Processing line... 781s CAC 781s CAC 781s Processing line... 781s GTG 781s GTG 781s Processing line... 781s CAC 781s CAC 781s Processing line... 781s Processing line... 781s GAA 781s GAA 781s Processing line... 781s TTC 781s TTC 781s Processing line... 781s TTC 781s TTC 781s Processing line... 781s Processing line... 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 12 alignments, 0 edits 781s --------------- 781s PASSED 781s ALSO checking that bowtie2 and bowtie2-align match up 781s /usr/bin/bowtie2 --rfg 29.8689578752319,15.3204355497086 --rdg 30.5639233607489,1.10058483227608 --score-min L,1.67949807213495,5.25701611295639 -k 4 --cp-ival 2 -D 15 --cp-min 9 -R 1 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 781s 20 reads; of these: 781s 20 (100.00%) were paired; of these: 781s 20 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 20 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 20 pairs aligned 0 times concordantly or discordantly; of these: 781s 40 mates make up the pairs; of these: 781s 33 (82.50%) aligned 0 times 781s 5 (12.50%) aligned exactly 1 time 781s 2 (5.00%) aligned >1 times 781s 17.50% overall alignment rate 781s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.1 781s Introducing 2 SNPs, 2/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.2 781s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s SNPs introduced: 6 781s Reference gaps introduced: 2 781s Read gaps introduced: 0 781s Rearrangements introduced: 1 781s Created read sampler 781s Sampling 93 reads 781s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 781s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 781s parsing sequence Sim.pm.1... 781s parsing sequence Sim.pm.2... 781s Parsed 86 reference bases 781s *** Run 12 of 100 781s /usr/bin/bowtie2 -k 2 --score-min L,5.10634811177831,5.1943322403907 --norc -R 3 --ma 38.2348315431553 -N 1 -L21 --cp-min 3 --n-ceil 1.43310427191382,0.111392570877619 --cp-ival 1 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 781s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 781s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (1) 781s Warning: skipping mate #1 of read '27' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 781s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (1) 781s Warning: skipping mate #2 of read '54' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 781s Read 50 alignments... 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 781s Warning: skipping mate #2 of read '84' because length (1) <= # seed mismatches (1) 781s Warning: skipping mate #2 of read '84' because it was < 2 characters long 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 781s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 781s Read 100 alignments... 781s 93 reads; of these: 781s 93 (100.00%) were paired; of these: 781s 93 (100.00%) aligned concordantly 0 times 781s 0 (0.00%) aligned concordantly exactly 1 time 781s 0 (0.00%) aligned concordantly >1 times 781s ---- 781s 93 pairs aligned concordantly 0 times; of these: 781s 0 (0.00%) aligned discordantly 1 time 781s ---- 781s 93 pairs aligned 0 times concordantly or discordantly; of these: 781s 186 mates make up the pairs; of these: 781s 174 (93.55%) aligned 0 times 781s 5 (2.69%) aligned exactly 1 time 781s 7 (3.76%) aligned >1 times 781s 6.45% overall alignment rate 781s Read 150 alignments... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TCC 781s TCC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TT 781s TT 781s Processing line... 781s TT 781s TT 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TGACTGGA 781s TGACTGGA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CCGC 781s CCGC 781s Processing line... 781s CCGC 781s CCGC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TGGATCTC 781s TGGATCTC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TGGATCT 781s TGGATCT 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CC 781s CC 781s Processing line... 781s CC 781s CC 781s Processing line... 781s Processing line... 781s AA 781s AA 781s Processing line... 781s AA 781s AA 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s GC 781s GC 781s Processing line... 781s GC 781s GC 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s CG 781s CG 781s Processing line... 781s CG 781s CG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s ACT 781s ACT 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s TG 781s TG 781s Processing line... 781s TG 781s TG 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s Processing line... 781s --- Summary --- 781s Read 1 reference strings 781s Checked 19 alignments, 0 edits 781s --------------- 781s PASSED 781s Flattened IUPAC characters 781s Mutating sequence Sim.pm.2 781s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutating sequence Sim.pm.1 781s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 781s Finished SNPs 781s Finished ref gaps 781s Finished read gaps 781s Mutated reference genome to subject genome 781s SNPs introduced: 7 781s Reference gaps introduced: 0 781s Read gaps introduced: 0 781s Rearrangements introduced: 0 781s Created read sampler 781s Sampling 112 reads 782s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 782s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 86 reference bases 782s *** Run 13 of 100 782s /usr/bin/bowtie2 --cp-min 3 --cp-ival 3 -D 30 --trim5 4 --score-min L,4.68941956646771,3.51798805130133 --norc --np 1 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 782s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 782s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '3' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 782s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '4' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 782s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '13' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 782s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '27' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 782s Warning: skipping read '28' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '28' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 782s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '29' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 782s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '31' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 782s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '33' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 782s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '46' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 782s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '52' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 782s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '57' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 782s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '59' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 782s Warning: skipping read '61' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '61' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 782s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '62' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 782s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '64' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 782s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '66' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 782s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '69' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 782s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '74' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 782s Warning: skipping read '80' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '80' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 782s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '84' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 782s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '85' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 782s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '90' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 782s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '91' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 782s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '93' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 782s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '99' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 782s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '104' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 782s 112 reads; of these: 782s 112 (100.00%) were unpaired; of these: 782s 94 (83.93%) aligned 0 times 782s 13 (11.61%) aligned exactly 1 time 782s 5 (4.46%) aligned >1 times 782s 16.07% overall alignment rate 782s Read 50 alignments... 782s Read 100 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TC 782s TC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GATCTCAA 782s GATCTCAA 782s Processing line... 782s Processing line... 782s Processing line... 782s CAACGG 782s CAACGG 782s Processing line... 782s GCCGCCACCCTCTTTCCCG 782s GCCGCCACCCTCTTTCCCG 782s Processing line... 782s Processing line... 782s Processing line... 782s AAAGGG 782s AAAGGG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGC 782s GGC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GCCACCG 782s GCCACCG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TC 782s TC 782s Processing line... 782s GTG 782s GTG 782s Processing line... 782s Processing line... 782s CGCCACCCT 782s CGCCACCCT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CGGCCGCCAC 782s CGGCCGCCAC 782s Processing line... 782s Processing line... 782s Processing line... 782s GCCACCGGGAG 782s GCCACCGGGAG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AC 782s AC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GTGCAATTCGAATCATGACTGGAT 782s GTGCAATTCGAATCATGACTGGAT 782s Processing line... 782s Processing line... 782s Processing line... 782s TCAT 782s TCAT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GATC 782s GATC 782s Processing line... 782s Processing line... 782s CT 782s CT 782s Processing line... 782s GTGCAATTCGAATCATGACTGGAT 782s GTGCAATTCGAATCATGACTGGAT 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 18 alignments, 0 edits 782s --------------- 782s PASSED 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.2 782s Introducing 4 SNPs, 1/0 ref/read gaps, and 3 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.1 782s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 7 782s Reference gaps introduced: 1 782s Read gaps introduced: 1 782s Rearrangements introduced: 3 782s Created read sampler 782s Sampling 124 reads 782s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 782s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 86 reference bases 782s *** Run 14 of 100 782s /usr/bin/bowtie2 --mm --score-min L,4.69505428852496,1.67799183150255 --rfg 12.27465097436 -R 3 --cp-min 9 --cp-ival 1 --ma 10.5831274704849 --mp 7.33532093442151,7.03327709288735 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 782s Warning: skipping mate #1 of read '4' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '4' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 782s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '11' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 782s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '28' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 782s Read 50 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 782s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '66' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 782s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '75' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 782s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '97' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 782s Warning: skipping mate #1 of read '103' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '103' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 782s Read 100 alignments... 782s Read 150 alignments... 782s Read 200 alignments... 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 782s Warning: skipping mate #2 of read '120' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '120' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 782s 124 reads; of these: 782s 124 (100.00%) were paired; of these: 782s 122 (98.39%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 2 (1.61%) aligned concordantly >1 times 782s ---- 782s 122 pairs aligned concordantly 0 times; of these: 782s 1 (0.82%) aligned discordantly 1 time 782s ---- 782s 121 pairs aligned 0 times concordantly or discordantly; of these: 782s 242 mates make up the pairs; of these: 782s 213 (88.02%) aligned 0 times 782s 18 (7.44%) aligned exactly 1 time 782s 11 (4.55%) aligned >1 times 782s 14.11% overall alignment rate 782s Read 250 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGCCACCGGGAGG 782s GGGCCACCGGGAGG 782s Processing line... 782s Processing line... 782s GCCACCGGGAGGC 782s GCCACCGGGAGGC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGAGGCA 782s GGGAGGCA 782s Processing line... 782s TGCAATTCGAATCATGA 782s TGCAATTCGAATCATGA 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGCCACCGGG 782s GGCCACCGGG 782s Processing line... 782s Processing line... 782s GC 782s GC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CACC 782s CACC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CAA 782s CAA 782s Processing line... 782s Processing line... 782s AGGGCCACCGGGAGGCA 782s AGGGCCACCGGGAGGCA 782s Processing line... 782s Processing line... 782s ATCATGACTGGATC 782s ATCATGACTGGATC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CCACCGG 782s CCACCGG 782s Processing line... 782s Processing line... 782s GGGCCACCGGGA 782s GGGCCACCGGGA 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GCAATTCGAATCATG 782s GCAATTCGAATCATG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGCCACCGGGAG 782s GGCCACCGGGAG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GAGGCAC 782s GAGGCAC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GA 782s GA 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGAGGCAC 782s GGGAGGCAC 782s Processing line... 782s Processing line... 782s ATCATGACTGGAT 782s ATCATGACTGGAT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AT 782s AT 782s Processing line... 782s CAAT 782s CAAT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AA 782s AA 782s Processing line... 782s GC 782s GC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AAGGGCCACCGGGAGGCAC 782s AAGGGCCACCGGGAGGCAC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s ATGA 782s ATGA 782s Processing line... 782s Processing line... 782s TGCAATTCGAAT 782s TGCAATTCGAAT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CGC 782s CGC 782s Processing line... 782s Processing line... 782s TG 782s TG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GCCACC 782s GCCACC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GGGCCA 782s GGGCCA 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s TGCAATTCGAATC 782s TGCAATTCGAATC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AGGC 782s AGGC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AT 782s AT 782s Processing line... 782s Processing line... 782s AAGGGCC 782s AAGGGCC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CC 782s CC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GA 782s GA 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 35 alignments, 0 edits 782s --------------- 782s PASSED 782s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 782s /usr/bin/bowtie2 --mm --score-min L,4.69505428852496,1.67799183150255 --rfg 12.27465097436 -R 3 --cp-min 9 --cp-ival 1 --ma 10.5831274704849 --mp 7.33532093442151,7.03327709288735 -r -p 4 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 782s Warning: skipping mate #1 of read '4' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '4' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 782s Warning: skipping mate #1 of read '11' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '11' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 782s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '28' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 782s Warning: skipping mate #1 of read '66' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '66' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 782s Warning: skipping mate #2 of read '75' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '75' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 782s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '97' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 782s Warning: skipping mate #1 of read '103' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '103' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 782s Warning: skipping mate #2 of read '120' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '120' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 782s 124 reads; of these: 782s 124 (100.00%) were paired; of these: 782s 122 (98.39%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 2 (1.61%) aligned concordantly >1 times 782s ---- 782s 122 pairs aligned concordantly 0 times; of these: 782s 1 (0.82%) aligned discordantly 1 time 782s ---- 782s 121 pairs aligned 0 times concordantly or discordantly; of these: 782s 242 mates make up the pairs; of these: 782s 213 (88.02%) aligned 0 times 782s 18 (7.44%) aligned exactly 1 time 782s 11 (4.55%) aligned >1 times 782s 14.11% overall alignment rate 782s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 782s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 782s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.2 782s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.1 782s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 5 782s Reference gaps introduced: 0 782s Read gaps introduced: 0 782s Rearrangements introduced: 0 782s Created read sampler 782s Sampling 78 reads 782s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 782s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 86 reference bases 782s *** Run 15 of 100 782s /usr/bin/bowtie2 --np 1 -i C,2.76885685061702 -M 2 --trim5 1 --cp-min 4 --score-min L,6.20402892601791,6.14370504543881 --local --cp-ival 1 -D 19 --nofw -N 1 -L26 --trim3 5 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 782s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 782s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '1' because it was < 2 characters long 782s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '4' because it was < 2 characters long 782s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '6' because it was < 2 characters long 782s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '7' because it was < 2 characters long 782s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 782s Warning: skipping read '8' because it was < 2 characters long 782s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '25' because it was < 2 characters long 782s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '26' because it was < 2 characters long 782s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 782s Warning: skipping read '44' because it was < 2 characters long 782s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '52' because it was < 2 characters long 782s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '55' because it was < 2 characters long 782s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '60' because it was < 2 characters long 782s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (1) 782s Warning: skipping mate #2 of read '61' because it was < 2 characters long 782s Read 50 alignments... 782s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '75' because it was < 2 characters long 782s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (1) 782s Warning: skipping mate #2 of read '76' because it was < 2 characters long 782s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '77' because it was < 2 characters long 782s Read 100 alignments... 782s 78 reads; of these: 782s 71 (91.03%) were paired; of these: 782s 71 (100.00%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 0 (0.00%) aligned concordantly >1 times 782s ---- 782s 71 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 71 pairs aligned 0 times concordantly or discordantly; of these: 782s 142 mates make up the pairs; of these: 782s 142 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 7 (8.97%) were unpaired; of these: 782s 7 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s Read 150 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 0 alignments, 0 edits 782s --------------- 782s PASSED 782s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 782s /usr/bin/bowtie2 --np 1 -i C,2.76885685061702 -M 2 --trim5 1 --cp-min 4 --score-min L,6.20402892601791,6.14370504543881 --local --cp-ival 1 -D 19 --nofw -N 1 -L26 --trim3 5 -r -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 782s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 782s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '1' because it was < 2 characters long 782s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '4' because it was < 2 characters long 782s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '6' because it was < 2 characters long 782s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '7' because it was < 2 characters long 782s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 782s Warning: skipping read '8' because it was < 2 characters long 782s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '25' because it was < 2 characters long 782s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '26' because it was < 2 characters long 782s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 782s Warning: skipping read '44' because it was < 2 characters long 782s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '52' because it was < 2 characters long 782s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '55' because it was < 2 characters long 782s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '60' because it was < 2 characters long 782s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (1) 782s Warning: skipping mate #2 of read '61' because it was < 2 characters long 782s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '75' because it was < 2 characters long 782s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (1) 782s Warning: skipping mate #2 of read '76' because it was < 2 characters long 782s Warning: skipping mate #1 of read '77' because length (1) <= # seed mismatches (1) 782s Warning: skipping mate #1 of read '77' because it was < 2 characters long 782s 78 reads; of these: 782s 71 (91.03%) were paired; of these: 782s 71 (100.00%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 0 (0.00%) aligned concordantly >1 times 782s ---- 782s 71 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 71 pairs aligned 0 times concordantly or discordantly; of these: 782s 142 mates make up the pairs; of these: 782s 142 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 7 (8.97%) were unpaired; of these: 782s 7 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.2 782s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.1 782s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 4 782s Reference gaps introduced: 0 782s Read gaps introduced: 1 782s Rearrangements introduced: 2 782s Created read sampler 782s Sampling 43 reads 782s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 782s *** Run 16 of 100 782s /usr/bin/bowtie2 --rfg 10.3538419767639 --rdg 11.4436496322557 --score-min L,2.40058087559853,3.93974961474478 --trim3 9 --cp-ival 3 --local --nofw -k 12 --trim5 6 --np 2 --cp-min 7 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 782s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 86 reference bases 782s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '0' because it was < 2 characters long 782s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '1' because it was < 2 characters long 782s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '2' because it was < 2 characters long 782s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '4' because it was < 2 characters long 782s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '6' because it was < 2 characters long 782s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '9' because it was < 2 characters long 782s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '10' because it was < 2 characters long 782s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '11' because it was < 2 characters long 782s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '13' because it was < 2 characters long 782s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '16' because it was < 2 characters long 782s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '23' because it was < 2 characters long 782s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '25' because it was < 2 characters long 782s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '27' because it was < 2 characters long 782s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '28' because it was < 2 characters long 782s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '30' because it was < 2 characters long 782s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '31' because it was < 2 characters long 782s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '32' because it was < 2 characters long 782s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '34' because it was < 2 characters long 782s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '39' because it was < 2 characters long 782s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '41' because it was < 2 characters long 782s 43 reads; of these: 782s 43 (100.00%) were unpaired; of these: 782s 43 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 0 alignments, 0 edits 782s --------------- 782s PASSED 782s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 782s /usr/bin/bowtie2 --rfg 10.3538419767639 --rdg 11.4436496322557 --score-min L,2.40058087559853,3.93974961474478 --trim3 9 --cp-ival 3 --local --nofw -k 12 --trim5 6 --np 2 --cp-min 7 -r -p 2 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 782s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '0' because it was < 2 characters long 782s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '1' because it was < 2 characters long 782s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '2' because it was < 2 characters long 782s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '4' because it was < 2 characters long 782s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '6' because it was < 2 characters long 782s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '9' because it was < 2 characters long 782s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '10' because it was < 2 characters long 782s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '11' because it was < 2 characters long 782s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '13' because it was < 2 characters long 782s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '16' because it was < 2 characters long 782s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '23' because it was < 2 characters long 782s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '25' because it was < 2 characters long 782s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '27' because it was < 2 characters long 782s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '28' because it was < 2 characters long 782s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '30' because it was < 2 characters long 782s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '31' because it was < 2 characters long 782s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '32' because it was < 2 characters long 782s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '34' because it was < 2 characters long 782s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '39' because it was < 2 characters long 782s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '41' because it was < 2 characters long 782s 43 reads; of these: 782s 43 (100.00%) were unpaired; of these: 782s 43 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 782s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 782s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.2 782s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.1 782s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 10 782s Reference gaps introduced: 0 782s Read gaps introduced: 0 782s Rearrangements introduced: 0 782s Created read sampler 782s Sampling 45 reads 782s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 782s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 86 reference bases 782s *** Run 17 of 100 782s /usr/bin/bowtie2 --score-min L,2.21431682874306,4.56526310278446 --np 7 --mm --ma 13.9821635729093 --cp-min 4 --n-ceil 0.266132090762829,0.409169464735037 --cp-ival 1 --trim3 6 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 782s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 782s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 782s Warning: skipping read '3' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 782s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 782s Warning: skipping mate #2 of read '19' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 782s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 782s Warning: skipping mate #1 of read '24' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 782s 45 reads; of these: 782s 40 (88.89%) were paired; of these: 782s 40 (100.00%) aligned concordantly 0 times 782s 0 (0.00%) aligned concordantly exactly 1 time 782s 0 (0.00%) aligned concordantly >1 times 782s ---- 782s 40 pairs aligned concordantly 0 times; of these: 782s 0 (0.00%) aligned discordantly 1 time 782s ---- 782s 40 pairs aligned 0 times concordantly or discordantly; of these: 782s 80 mates make up the pairs; of these: 782s 76 (95.00%) aligned 0 times 782s 3 (3.75%) aligned exactly 1 time 782s 1 (1.25%) aligned >1 times 782s 5 (11.11%) were unpaired; of these: 782s 5 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 4.71% overall alignment rate 782s Read 50 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AAAGGGCCAC 782s AAAGGGCCAC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CAT 782s CAT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s CATGACTGGAT 782s CATGACTGGAT 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AAAGGGCCA 782s AAAGGGCCA 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 4 alignments, 0 edits 782s --------------- 782s PASSED 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.1 782s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.2 782s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 10 782s Reference gaps introduced: 0 782s Read gaps introduced: 1 782s Rearrangements introduced: 0 782s Created read sampler 782s Sampling 16 reads 782s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 782s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 86 reference bases 782s *** Run 18 of 100 782s /usr/bin/bowtie2 --ma 25.9132154903483 --cp-min 3 --cp-ival 1 --score-min L,8.19113418657631,7.07086950681354 --rfg 49.2136187302683 --rdg 28.2215828354631 --np 7 --gbar 4 --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 782s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 782s 16 reads; of these: 782s 16 (100.00%) were unpaired; of these: 782s 11 (68.75%) aligned 0 times 782s 2 (12.50%) aligned exactly 1 time 782s 3 (18.75%) aligned >1 times 782s 31.25% overall alignment rate 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GAATCATG 782s GAATCATG 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s AC 782s AC 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s GAATCATGA 782s GAATCATGA 782s Processing line... 782s CA 782s CA 782s Processing line... 782s TC 782s TC 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 5 alignments, 0 edits 782s --------------- 782s PASSED 782s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 782s /usr/bin/bowtie2 --ma 25.9132154903483 --cp-min 3 --cp-ival 1 --score-min L,8.19113418657631,7.07086950681354 --rfg 49.2136187302683 --rdg 28.2215828354631 --np 7 --gbar 4 --qseq -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 782s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 782s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 782s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 782s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 782s 16 reads; of these: 782s 16 (100.00%) were unpaired; of these: 782s 11 (68.75%) aligned 0 times 782s 2 (12.50%) aligned exactly 1 time 782s 3 (18.75%) aligned >1 times 782s 31.25% overall alignment rate 782s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.2 782s Introducing 8 SNPs, 0/0 ref/read gaps, and 2 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.1 782s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 13 782s Reference gaps introduced: 1 782s Read gaps introduced: 0 782s Rearrangements introduced: 2 782s Created read sampler 782s Sampling 133 reads 782s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 782s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 86 reference bases 782s *** Run 19 of 100 782s /usr/bin/bowtie2 -M 2 --cp-min 4 --mm --score-min L,4.61947739713619,5.63898087633465 --rfg 49.9549016063878,14.486775817059 --cp-ival 1 --local --n-ceil 0.574879444839784,0.18598734834647 --nofw -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 782s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 782s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '23' because it was < 2 characters long 782s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '92' because it was < 2 characters long 782s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '111' because it was < 2 characters long 782s 133 reads; of these: 782s 133 (100.00%) were unpaired; of these: 782s 133 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s Read 50 alignments... 782s Read 100 alignments... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s Processing line... 782s --- Summary --- 782s Read 1 reference strings 782s Checked 0 alignments, 0 edits 782s --------------- 782s PASSED 782s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 782s /usr/bin/bowtie2 -M 2 --cp-min 4 --mm --score-min L,4.61947739713619,5.63898087633465 --rfg 49.9549016063878,14.486775817059 --cp-ival 1 --local --n-ceil 0.574879444839784,0.18598734834647 --nofw -f -p 4 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 782s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 782s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '23' because it was < 2 characters long 782s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '92' because it was < 2 characters long 782s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '111' because it was < 2 characters long 782s 133 reads; of these: 782s 133 (100.00%) were unpaired; of these: 782s 133 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 782s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 782s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 782s /usr/bin/bowtie2 -M 2 --cp-min 4 --mm --score-min L,4.61947739713619,5.63898087633465 --rfg 49.9549016063878,14.486775817059 --cp-ival 1 --local --n-ceil 0.574879444839784,0.18598734834647 --nofw -f -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 782s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 782s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 782s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '23' because it was < 2 characters long 782s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '92' because it was < 2 characters long 782s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 782s Warning: skipping read '111' because it was < 2 characters long 782s 133 reads; of these: 782s 133 (100.00%) were unpaired; of these: 782s 133 (100.00%) aligned 0 times 782s 0 (0.00%) aligned exactly 1 time 782s 0 (0.00%) aligned >1 times 782s 0.00% overall alignment rate 782s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 782s Flattened IUPAC characters 782s Mutating sequence Sim.pm.1 782s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutating sequence Sim.pm.2 782s Introducing 3 SNPs, 1/1 ref/read gaps, and 1 rearrangements 782s Finished SNPs 782s Finished ref gaps 782s Finished read gaps 782s Mutated reference genome to subject genome 782s SNPs introduced: 3 782s Reference gaps introduced: 1 782s Read gaps introduced: 1 782s Rearrangements introduced: 2 782s Created read sampler 782s Sampling 181 reads 782s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 782s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 782s parsing sequence Sim.pm.1... 782s parsing sequence Sim.pm.2... 782s Parsed 86 reference bases 782s *** Run 20 of 100 782s /usr/bin/bowtie2 -R 3 --mp 6.63500729341787,1.52651756664458 --cp-ival 1 --cp-min 6 --mm --trim5 8 -k 3 --score-min L,9.37641788273841,3.65253029273128 --gbar 5 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 783s Read 50 alignments... 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 783s Warning: skipping mate #2 of read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 783s Read 100 alignments... 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 783s Warning: skipping mate #2 of read 'R_1_1_1_134_134_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 783s Warning: skipping mate #2 of read 'R_1_1_1_137_137_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_141_141_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_144_144_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 783s Warning: skipping mate #2 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_166_166_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_167_167_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_169_169_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 783s Warning: skipping mate #2 of read 'R_1_1_1_170_170_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_170_170_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_181_181_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_181_181_1/1' because it was < 2 characters long 783s Read 150 alignments... 783s 181 reads; of these: 783s 142 (78.45%) were paired; of these: 783s 142 (100.00%) aligned concordantly 0 times 783s 0 (0.00%) aligned concordantly exactly 1 time 783s 0 (0.00%) aligned concordantly >1 times 783s ---- 783s 142 pairs aligned concordantly 0 times; of these: 783s 0 (0.00%) aligned discordantly 1 time 783s ---- 783s 142 pairs aligned 0 times concordantly or discordantly; of these: 783s 284 mates make up the pairs; of these: 783s 262 (92.25%) aligned 0 times 783s 13 (4.58%) aligned exactly 1 time 783s 9 (3.17%) aligned >1 times 783s 39 (21.55%) were unpaired; of these: 783s 37 (94.87%) aligned 0 times 783s 1 (2.56%) aligned exactly 1 time 783s 1 (2.56%) aligned >1 times 783s 7.43% overall alignment rate 783s Read 200 alignments... 783s Read 250 alignments... 783s Read 300 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AATTCGAATCATGACTGGATCTCAAAT 783s AATTCGAATCATGACTGGATCTCAAAT 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GGG 783s GGG 783s Processing line... 783s CCC 783s CCC 783s Processing line... 783s GGG 783s GGG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s CTT 783s CTT 783s Processing line... 783s AAG 783s AAG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s CCACCGGGAGGCA 783s CCACCGGGAGGCA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s CCACCG 783s CCACCG 783s Processing line... 783s Processing line... 783s ATC 783s ATC 783s Processing line... 783s ATC 783s ATC 783s Processing line... 783s ATC 783s ATC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TCGAATCA 783s TCGAATCA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ACCCT 783s ACCCT 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s CCACCGGGA 783s CCACCGGGA 783s Processing line... 783s Processing line... 783s CAT 783s CAT 783s Processing line... 783s ATG 783s ATG 783s Processing line... 783s Processing line... 783s CCACCGGGAGGC 783s CCACCGGGAGGC 783s Processing line... 783s Processing line... 783s Processing line... 783s CTC 783s CTC 783s Processing line... 783s CTC 783s CTC 783s Processing line... 783s GAG 783s GAG 783s Processing line... 783s TTCGAATCATGACTGGATCTC 783s TTCGAATCATGACTGGATCTC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GGGAG 783s GGGAG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AA 783s AA 783s Processing line... 783s AA 783s AA 783s Processing line... 783s AA 783s AA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TTCCC 783s TTCCC 783s Processing line... 783s Processing line... 783s CC 783s CC 783s Processing line... 783s CC 783s CC 783s Processing line... 783s CC 783s CC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TGC 783s TGC 783s Processing line... 783s GCA 783s GCA 783s Processing line... 783s GCA 783s GCA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TTCGAATCATGACTGGATCTCAAA 783s TTCGAATCATGACTGGATCTCAAA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TCGAATCATGACTGGATCT 783s TCGAATCATGACTGGATCT 783s Processing line... 783s AA 783s AA 783s Processing line... 783s AA 783s AA 783s Processing line... 783s AA 783s AA 783s Processing line... 783s Processing line... 783s TGGA 783s TGGA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s CAA 783s CAA 783s Processing line... 783s CAA 783s CAA 783s Processing line... 783s CAA 783s CAA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s CCGGGAGG 783s CCGGGAGG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s /usr/bin/bowtie2 -R 3 --mp 6.63500729341787,1.52651756664458 --cp-ival 1 --cp-min 6 --mm --trim5 8 -k 3 --score-min L,9.37641788273841,3.65253029273128 --gbar 5 --qseq -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 42 alignments, 0 edits 783s --------------- 783s PASSED 783s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 783s Warning: skipping mate #2 of read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 783s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_124_124_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_145_145_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_146_146_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_146_146_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_147_147_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_148_148_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_148_148_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_149_149_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_150_150_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_151_151_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_152_152_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_153_153_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_154_154_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_155_155_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_156_156_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_157_157_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_158_158_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_159_159_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_160_160_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_161_161_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_162_162_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_163_163_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_164_164_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_165_165_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_166_166_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_167_167_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_167_167_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_168_168_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_168_168_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_169_169_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_170_170_1/1; setting to 0 instead 783s Warning: skipping mate #2 of read 'R_1_1_1_170_170_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_170_170_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_171_171_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_172_172_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_173_173_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_174_174_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_175_175_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_176_176_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_177_177_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_178_178_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_179_179_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_180_180_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_181_181_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_181_181_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_181_181_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_133_133_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 783s Warning: skipping mate #2 of read 'R_1_1_1_134_134_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_134_134_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_136_136_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_136_136_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 783s Warning: skipping mate #2 of read 'R_1_1_1_137_137_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_137_137_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_141_141_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_141_141_1/1' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 783s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_144_144_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 783s Warning: skipping mate #2 of read 'R_1_1_1_144_144_1/1' because it was < 2 characters long 783s 181 reads; of these: 783s 142 (78.45%) were paired; of these: 783s 142 (100.00%) aligned concordantly 0 times 783s 0 (0.00%) aligned concordantly exactly 1 time 783s 0 (0.00%) aligned concordantly >1 times 783s ---- 783s 142 pairs aligned concordantly 0 times; of these: 783s 0 (0.00%) aligned discordantly 1 time 783s ---- 783s 142 pairs aligned 0 times concordantly or discordantly; of these: 783s 284 mates make up the pairs; of these: 783s 262 (92.25%) aligned 0 times 783s 13 (4.58%) aligned exactly 1 time 783s 9 (3.17%) aligned >1 times 783s 39 (21.55%) were unpaired; of these: 783s 37 (94.87%) aligned 0 times 783s 1 (2.56%) aligned exactly 1 time 783s 1 (2.56%) aligned >1 times 783s 7.43% overall alignment rate 783s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.1 783s Introducing 9 SNPs, 0/1 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.2 783s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 12 783s Reference gaps introduced: 0 783s Read gaps introduced: 1 783s Rearrangements introduced: 0 783s Created read sampler 783s Sampling 51 reads 783s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 783s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 86 reference bases 783s *** Run 21 of 100 783s /usr/bin/bowtie2 -a --mm --score-min L,7.62334533407556,1.36129106241732 --rdg 35.8012424377285 --rfg 37.5302879028369 --cp-ival 1 --local --np 2 --cp-min 3 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 783s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '20' because it was < 2 characters long 783s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '43' because it was < 2 characters long 783s 51 reads; of these: 783s 51 (100.00%) were unpaired; of these: 783s 48 (94.12%) aligned 0 times 783s 3 (5.88%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 5.88% overall alignment rate 783s Read 50 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GTGCAATTCGAATCATGACT 783s GTGCAATTCGAATCATGACT 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TTCGAATCATGACTGGA 783s TTCGAATCATGACTGGA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ATCATGACTGG 783s ATCATGACTGG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 3 alignments, 0 edits 783s --------------- 783s PASSED 783s ALSO checking that bowtie2 and bowtie2-align match up 783s /usr/bin/bowtie2 -a --mm --score-min L,7.62334533407556,1.36129106241732 --rdg 35.8012424377285 --rfg 37.5302879028369 --cp-ival 1 --local --np 2 --cp-min 3 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 783s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '20' because it was < 2 characters long 783s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '43' because it was < 2 characters long 783s 51 reads; of these: 783s 51 (100.00%) were unpaired; of these: 783s 48 (94.12%) aligned 0 times 783s 3 (5.88%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 5.88% overall alignment rate 783s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 783s /usr/bin/bowtie2 -a --mm --score-min L,7.62334533407556,1.36129106241732 --rdg 35.8012424377285 --rfg 37.5302879028369 --cp-ival 1 --local --np 2 --cp-min 3 -r -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 783s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 783s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '20' because it was < 2 characters long 783s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '43' because it was < 2 characters long 783s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 783s 51 reads; of these: 783s 51 (100.00%) were unpaired; of these: 783s 48 (94.12%) aligned 0 times 783s 3 (5.88%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 5.88% overall alignment rate 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.1 783s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.2 783s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 7 783s Reference gaps introduced: 0 783s Read gaps introduced: 0 783s Rearrangements introduced: 0 783s Created read sampler 783s Sampling 104 reads 783s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 783s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 86 reference bases 783s *** Run 22 of 100 783s /usr/bin/bowtie2 -a --mm --score-min L,7.80091410320145,4.67045297845663 --rdg 20.8779545373405,13.5250319501514 --cp-min 2 --cp-ival 1 --local -N 0 -L23 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 783s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '35' because it was < 2 characters long 783s 104 reads; of these: 783s 104 (100.00%) were unpaired; of these: 783s 104 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s Read 50 alignments... 783s Read 100 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 0 alignments, 0 edits 783s --------------- 783s PASSED 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.2 783s *** Run 23 of 100 783s /usr/bin/bowtie2 --trim5 0 -k 5 --rfg 31.4216991466677 --score-min L,4.08416907869017,2.71662939848076 --np 12 -R 1 --ma 8.91479896137394 --cp-ival 2 --cp-min 3 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 783s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.1 783s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 3 783s Reference gaps introduced: 0 783s Read gaps introduced: 2 783s Rearrangements introduced: 1 783s Created read sampler 783s Sampling 226 reads 783s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 783s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 86 reference bases 783s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 783s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 783s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '19' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 783s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '41' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 783s Warning: skipping read '75' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '75' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 783s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '96' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 783s Read 50 alignments... 783s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 783s Read 100 alignments... 783s Read 150 alignments... 783s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '193; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '194; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '195; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '196; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '197; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '198; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '199; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '200; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '201; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '202; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '203; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '204; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '205; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '206; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '207; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '208; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '209; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '210; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '211; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '212; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '213; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '214; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '215; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '216; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '217; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '218; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '219; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '220; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '221; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '222; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '223; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '224; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '225; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '226; setting to 0 instead 783s 226 reads; of these: 783s 226 (100.00%) were unpaired; of these: 783s 158 (69.91%) aligned 0 times 783s 52 (23.01%) aligned exactly 1 time 783s 16 (7.08%) aligned >1 times 783s 30.09% overall alignment rate 783s Read 200 alignments... 783s Read 250 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GGCCACCGGGAGGCAC 783s GGCCACCGGGAGGCAC 783s Processing line... 783s Processing line... 783s CATGAC 783s CATGAC 783s Processing line... 783s TGGATCTCA 783s TGGATCTCA 783s Processing line... 783s Processing line... 783s AA 783s AA 783s Processing line... 783s AA 783s AA 783s Processing line... 783s AA 783s AA 783s Processing line... 783s AA 783s AA 783s Processing line... 783s AA 783s AA 783s Processing line... 783s Processing line... 783s AAAGGGCCACCG 783s AAAGGGCCACCG 783s Processing line... 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TGACTGGATCT 783s TGACTGGATCT 783s Processing line... 783s GGCCACC 783s GGCCACC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AATTCGAATCATGACTGGATC 783s AATTCGAATCATGACTGGATC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ACGGC 783s ACGGC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AATTCGAATCATGACTGG 783s AATTCGAATCATGACTGG 783s Processing line... 783s Processing line... 783s TCG 783s TCG 783s Processing line... 783s CGA 783s CGA 783s Processing line... 783s TCG 783s TCG 783s Processing line... 783s ACTGGATC 783s ACTGGATC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TGTGCAATTCGAATCATGACTGGAT 783s TGTGCAATTCGAATCATGACTGGAT 783s Processing line... 783s Processing line... 783s Processing line... 783s TCTCAA 783s TCTCAA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ACCCTC 783s ACCCTC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s CG 783s CG 783s Processing line... 783s GGGAGGCAC 783s GGGAGGCAC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TGT 783s TGT 783s Processing line... 783s Processing line... 783s ATTCGAATCATGA 783s ATTCGAATCATGA 783s Processing line... 783s Processing line... 783s CCTCTTTCCC 783s CCTCTTTCCC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AATTCGAATCATGACTGGATCTCAA 783s AATTCGAATCATGACTGGATCTCAA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ATGACT 783s ATGACT 783s Processing line... 783s CAACGGCCG 783s CAACGGCCG 783s Processing line... 783s ATGACTGGATCT 783s ATGACTGGATCT 783s Processing line... 783s ATTCGAATCATGAC 783s ATTCGAATCATGAC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AA 783s AA 783s Processing line... 783s TT 783s TT 783s Processing line... 783s TT 783s TT 783s Processing line... 783s AA 783s AA 783s Processing line... 783s TT 783s TT 783s Processing line... 783s Processing line... 783s GCCGCCACCCTCT 783s GCCGCCACCCTCT 783s Processing line... 783s Processing line... 783s Processing line... 783s CTTTC 783s CTTTC 783s Processing line... 783s ACTGGATC 783s ACTGGATC 783s Processing line... 783s Processing line... 783s CC 783s CC 783s Processing line... 783s CC 783s CC 783s Processing line... 783s CC 783s CC 783s Processing line... 783s CC 783s CC 783s Processing line... 783s CC 783s CC 783s Processing line... 783s Processing line... 783s TGTGC 783s TGTGC 783s Processing line... 783s Processing line... 783s Processing line... 783s CAACGGC 783s CAACGGC 783s Processing line... 783s Processing line... 783s AAAT 783s AAAT 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AATCATGACTGGATCTCA 783s AATCATGACTGGATCTCA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s ACCCT 783s ACCCT 783s Processing line... 783s GGCCACCGGGAGGCA 783s GGCCACCGGGAGGCA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GGC 783s GGC 783s Processing line... 783s GCC 783s GCC 783s Processing line... 783s GCC 783s GCC 783s Processing line... 783s GCC 783s GCC 783s Processing line... 783s GGC 783s GGC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TGTGCAATTCGAATCATGACTG 783s TGTGCAATTCGAATCATGACTG 783s Processing line... 783s Processing line... 783s TC 783s TC 783s Processing line... 783s TC 783s TC 783s Processing line... 783s TC 783s TC 783s Processing line... 783s TC 783s TC 783s Processing line... 783s TC 783s TC 783s Processing line... 783s Processing line... 783s Processing line... 783s CGAATCA 783s CGAATCA 783s Processing line... 783s GAATCATGACTGGATCTCAA 783s GAATCATGACTGGATCTCAA 783s Processing line... 783s Processing line... 783s Processing line... 783s CGAATCATG 783s CGAATCATG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TCTC 783s TCTC 783s Processing line... 783s Processing line... 783s CCACCCTCTTT 783s CCACCCTCTTT 783s Processing line... 783s Processing line... 783s TCATG 783s TCATG 783s Processing line... 783s CATGA 783s CATGA 783s Processing line... 783s Processing line... 783s CTGGATCT 783s CTGGATCT 783s Processing line... 783s CAATTCGAATCATGACTG 783s CAATTCGAATCATGACTG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AAGGGCCA 783s AAGGGCCA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GCC 783s GCC 783s Processing line... 783s GCC 783s GCC 783s Processing line... 783s GGC 783s GGC 783s Processing line... 783s GCC 783s GCC 783s Processing line... 783s GGC 783s GGC 783s Processing line... 783s Processing line... 783s GGCAC 783s GGCAC 783s Processing line... 783s CCGGGA 783s CCGGGA 783s Processing line... 783s Processing line... 783s Processing line... 783s AGGCAC 783s AGGCAC 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s TGTGCAATTCGAA 783s TGTGCAATTCGAA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s AC 783s AC 783s Processing line... 783s GT 783s GT 783s Processing line... 783s AC 783s AC 783s Processing line... 783s CATGACTGGATCTCAAA 783s CATGACTGGATCTCAAA 783s Processing line... 783s GTGCAATT 783s GTGCAATT 783s Processing line... 783s GACTGGATCTCAAA 783s GACTGGATCTCAAA 783s Processing line... 783s ATCATGA 783s ATCATGA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GGCCACCGGGAGGCAC 783s GGCCACCGGGAGGCAC 783s Processing line... 783s Processing line... 783s TGTGCAATTCGAATCATGACTGGATCTCAA 783s TGTGCAATTCGAATCATGACTGGATCTCAA 783s Processing line... 783s CGGCCGCCACCCTC 783s CGGCCGCCACCCTC 783s Processing line... 783s Processing line... 783s Processing line... 783s AATCATGACTGGATCTCAA 783s AATCATGACTGGATCTCAA 783s Processing line... 783s AAG 783s AAG 783s Processing line... 783s CTT 783s CTT 783s Processing line... 783s Processing line... 783s CA 783s CA 783s Processing line... 783s CA 783s CA 783s Processing line... 783s CA 783s CA 783s Processing line... 783s CA 783s CA 783s Processing line... 783s CA 783s CA 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s GG 783s GG 783s Processing line... 783s GG 783s GG 783s Processing line... 783s GG 783s GG 783s Processing line... 783s GG 783s GG 783s Processing line... 783s GG 783s GG 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 124 alignments, 0 edits 783s --------------- 783s PASSED 783s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 783s /usr/bin/bowtie2 --trim5 0 -k 5 --rfg 31.4216991466677 --score-min L,4.08416907869017,2.71662939848076 --np 12 -R 1 --ma 8.91479896137394 --cp-ival 2 --cp-min 3 -q -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 783s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 783s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 783s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '19' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 783s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '41' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 783s Warning: skipping read '75' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '75' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 783s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '96' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '167; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '168; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '170; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '171; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '172; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '173; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '174; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '175; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '177; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '178; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '179; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '180; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '181; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '182; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '183; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '184; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '185; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '186; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '187; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '189; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '190; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '191; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '192; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '193; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '194; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '195; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '196; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '197; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '198; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '199; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '200; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '201; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '202; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '203; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '204; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '205; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '206; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '207; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '208; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '209; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '210; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '211; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '212; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '213; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '214; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '215; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '216; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '217; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '218; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '219; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '220; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '221; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '222; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '223; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '224; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '225; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '226; setting to 0 instead 783s 226 reads; of these: 783s 226 (100.00%) were unpaired; of these: 783s 158 (69.91%) aligned 0 times 783s 52 (23.01%) aligned exactly 1 time 783s 16 (7.08%) aligned >1 times 783s 30.09% overall alignment rate 783s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.1 783s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.2 783s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 2 783s Reference gaps introduced: 1 783s Read gaps introduced: 1 783s Rearrangements introduced: 0 783s Created read sampler 783s Sampling 99 reads 783s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 783s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 86 reference bases 783s *** Run 24 of 100 783s /usr/bin/bowtie2 --cp-min 9 --mm --rdg 47.0858808636199,17.6771724385022 --score-min L,3.14427162579405,8.04290601501568 --trim3 3 --cp-ival 1 --n-ceil 0.764885433258145,0.722905265375482 --local --mp 6.55089246520114,1.5413642227724 -N 0 -L25 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 783s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 783s Read 50 alignments... 783s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 783s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 783s Read 100 alignments... 783s 99 reads; of these: 783s 93 (93.94%) were paired; of these: 783s 93 (100.00%) aligned concordantly 0 times 783s 0 (0.00%) aligned concordantly exactly 1 time 783s 0 (0.00%) aligned concordantly >1 times 783s ---- 783s 93 pairs aligned concordantly 0 times; of these: 783s 0 (0.00%) aligned discordantly 1 time 783s ---- 783s 93 pairs aligned 0 times concordantly or discordantly; of these: 783s 186 mates make up the pairs; of these: 783s 186 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 6 (6.06%) were unpaired; of these: 783s 6 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s Read 150 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 0 alignments, 0 edits 783s --------------- 783s PASSED 783s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 783s /usr/bin/bowtie2 --cp-min 9 --mm --rdg 47.0858808636199,17.6771724385022 --score-min L,3.14427162579405,8.04290601501568 --trim3 3 --cp-ival 1 --n-ceil 0.764885433258145,0.722905265375482 --local --mp 6.55089246520114,1.5413642227724 -N 0 -L25 --qseq -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 783s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 783s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because length (1) <= # seed mismatches (0) 783s Warning: skipping mate #2 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 783s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 783s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 783s 99 reads; of these: 783s 93 (93.94%) were paired; of these: 783s 93 (100.00%) aligned concordantly 0 times 783s 0 (0.00%) aligned concordantly exactly 1 time 783s 0 (0.00%) aligned concordantly >1 times 783s ---- 783s 93 pairs aligned concordantly 0 times; of these: 783s 0 (0.00%) aligned discordantly 1 time 783s ---- 783s 93 pairs aligned 0 times concordantly or discordantly; of these: 783s 186 mates make up the pairs; of these: 783s 186 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 6 (6.06%) were unpaired; of these: 783s 6 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.1 783s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.2 783s Introducing 11 SNPs, 0/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 12 783s Reference gaps introduced: 0 783s Read gaps introduced: 0 783s Rearrangements introduced: 0 783s Created read sampler 783s Sampling 122 reads 783s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 783s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 86 reference bases 783s *** Run 25 of 100 783s /usr/bin/bowtie2 -N 1 -L25 --nofw -D 26 --cp-ival 1 --local --rdg 49.4880603274727 --score-min L,2.66059229157415,6.52359908470229 --gbar 4 --cp-min 5 -M 3 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 783s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 783s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (1) 783s Warning: skipping mate #1 of read '10' because it was < 2 characters long 783s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (1) 783s Warning: skipping mate #1 of read '64' because it was < 2 characters long 783s Read 50 alignments... 783s Warning: skipping mate #1 of read '104' because length (1) <= # seed mismatches (1) 783s Warning: skipping mate #1 of read '104' because it was < 2 characters long 783s Warning: skipping mate #1 of read '114' because length (1) <= # seed mismatches (1) 783s Warning: skipping mate #1 of read '114' because it was < 2 characters long 783s Read 100 alignments... 783s 122 reads; of these: 783s 122 (100.00%) were paired; of these: 783s 122 (100.00%) aligned concordantly 0 times 783s 0 (0.00%) aligned concordantly exactly 1 time 783s 0 (0.00%) aligned concordantly >1 times 783s ---- 783s 122 pairs aligned concordantly 0 times; of these: 783s 0 (0.00%) aligned discordantly 1 time 783s ---- 783s 122 pairs aligned 0 times concordantly or discordantly; of these: 783s 244 mates make up the pairs; of these: 783s 244 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s Read 150 alignments... 783s Read 200 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s 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line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 0 alignments, 0 edits 783s --------------- 783s PASSED 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.2 783s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.1 783s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 6 783s Reference gaps introduced: 1 783s Read gaps introduced: 0 783s Rearrangements introduced: 0 783s Created read sampler 783s Sampling 72 reads 783s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 783s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 86 reference bases 783s *** Run 26 of 100 783s /usr/bin/bowtie2 -k 5 -i C,4.73898925251052,5.52907440623796 --trim5 4 --np 4 --norc --cp-min 4 --gbar 2 --rfg 16.0605934086025 --score-min L,7.40066915427189,9.26121842172163 --trim3 0 --local --cp-ival 1 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 783s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '2' because it was < 2 characters long 783s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '10' because it was < 2 characters long 783s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '24' because it was < 2 characters long 783s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '35' because it was < 2 characters long 783s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '38' because it was < 2 characters long 783s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '50' because it was < 2 characters long 783s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '54' because it was < 2 characters long 783s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '66' because it was < 2 characters long 783s 72 reads; of these: 783s 72 (100.00%) were unpaired; of these: 783s 72 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s Read 50 alignments... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s /usr/bin/bowtie2 -k 5 -i C,4.73898925251052,5.52907440623796 --trim5 4 --np 4 --norc --cp-min 4 --gbar 2 --rfg 16.0605934086025 --score-min L,7.40066915427189,9.26121842172163 --trim3 0 --local --cp-ival 1 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s Processing line... 783s --- Summary --- 783s Read 1 reference strings 783s Checked 0 alignments, 0 edits 783s --------------- 783s PASSED 783s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 783s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '2' because it was < 2 characters long 783s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '10' because it was < 2 characters long 783s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '24' because it was < 2 characters long 783s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '35' because it was < 2 characters long 783s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '38' because it was < 2 characters long 783s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '50' because it was < 2 characters long 783s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 783s Warning: skipping read '54' because it was < 2 characters long 783s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 783s Warning: skipping read '66' because it was < 2 characters long 783s 72 reads; of these: 783s 72 (100.00%) were unpaired; of these: 783s 72 (100.00%) aligned 0 times 783s 0 (0.00%) aligned exactly 1 time 783s 0 (0.00%) aligned >1 times 783s 0.00% overall alignment rate 783s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 783s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 783s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 783s Flattened IUPAC characters 783s Mutating sequence Sim.pm.1 783s Introducing 5 SNPs, 0/2 ref/read gaps, and 1 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutating sequence Sim.pm.2 783s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 783s Finished SNPs 783s Finished ref gaps 783s Finished read gaps 783s Mutated reference genome to subject genome 783s SNPs introduced: 12 783s Reference gaps introduced: 0 783s Read gaps introduced: 3 783s Rearrangements introduced: 1 783s Created read sampler 783s Sampling 103 reads 783s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 783s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 783s parsing sequence Sim.pm.1... 783s parsing sequence Sim.pm.2... 783s Parsed 86 reference bases 783s *** Run 27 of 100 783s /usr/bin/bowtie2 --cp-ival 1 -D 7 -N 1 -L17 --mp 8.05427408060678,3.7385679966669 --gbar 4 --score-min L,1.37056688754735,3.03606647349226 --mm --cp-min 4 --ma 33.2416089417118 -i C,4.82173562974088 -M 4 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 783s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 783s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 783s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 783s Warning: skipping read '45' because length (1) <= # seed mismatches (1) 783s Warning: skipping read '45' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 783s Warning: skipping read '54' because length (1) <= # seed mismatches (1) 783s Warning: skipping read '54' because it was < 2 characters long 783s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 783s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 783s Warning: skipping read '79' because length (1) <= # seed mismatches (1) 783s Warning: skipping read '79' because it was < 2 characters long 784s /usr/bin/bowtie2 --cp-ival 1 -D 7 -N 1 -L17 --mp 8.05427408060678,3.7385679966669 --gbar 4 --score-min L,1.37056688754735,3.03606647349226 --mm --cp-min 4 --ma 33.2416089417118 -i C,4.82173562974088 -M 4 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 784s 103 reads; of these: 784s 103 (100.00%) were unpaired; of these: 784s 90 (87.38%) aligned 0 times 784s 9 (8.74%) aligned exactly 1 time 784s 4 (3.88%) aligned >1 times 784s 12.62% overall alignment rate 784s Read 50 alignments... 784s Read 100 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ACCC 784s ACCC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CCCTCT 784s CCCTCT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GATCTCAA 784s GATCTCAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AAAGGG 784s AAAGGG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GC 784s GC 784s Processing line... 784s Processing line... 784s Processing line... 784s TCG 784s TCG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATGACTGGA 784s ATGACTGGA 784s Processing line... 784s TGTGC 784s TGTGC 784s Processing line... 784s Processing line... 784s Processing line... 784s CAACGGCCGCCA 784s CAACGGCCGCCA 784s Processing line... 784s GA 784s GA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AGGGCCACC 784s AGGGCCACC 784s Processing line... 784s Processing line... 784s Processing line... 784s CG 784s CG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CTCA 784s CTCA 784s --- Summary --- 784s Read 1 reference strings 784s Checked 13 alignments, 0 edits 784s --------------- 784s PASSED 784s ALSO checking that bowtie2 and bowtie2-align match up 784s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 784s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 784s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: skipping read '45' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '45' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: skipping read '54' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '54' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read 'diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 784s /usr/bin/bowtie2 --cp-ival 1 -D 7 -N 1 -L17 --mp 8.05427408060678,3.7385679966669 --gbar 4 --score-min L,1.37056688754735,3.03606647349226 --mm --cp-min 4 --ma 33.2416089417118 -i C,4.82173562974088 -M 4 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 784s 72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 784s Warning: skipping read '79' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '79' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 784s 103 reads; of these: 784s 103 (100.00%) were unpaired; of these: 784s 90 (87.38%) aligned 0 times 784s 9 (8.74%) aligned exactly 1 time 784s 4 (3.88%) aligned >1 times 784s 12.62% overall alignment rate 784s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 784s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 784s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 784s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: skipping read '45' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '45' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: skipping read '54' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '54' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 784s Warning: skipping read '79' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '79' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 784s 103 reads; of these: 784s 103 (100.00%) were unpaired; of these: 784s 90 (87.38%) aligned 0 times 784s 9 (8.74%) aligned exactly 1 time 784s 4 (3.88%) aligned >1 times 784s 12.62% overall alignment rate 784s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 784s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 784s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.1 784s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s *** Run 28 of 100 784s /usr/bin/bowtie2 --score-min L,2.27334188727385,5.12469200398718 --mm -N 1 -L17 --mp 9.47994892103396,1.52523335844504 --cp-min 5 --cp-ival 2 --trim3 8 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 784s Mutating sequence Sim.pm.2 784s Introducing 0 SNPs, 0/0 ref/read gaps, and 2 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 1 784s Reference gaps introduced: 0 784s Read gaps introduced: 0 784s Rearrangements introduced: 2 784s Created read sampler 784s Sampling 87 reads 784s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 784s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 784s parsing sequence Sim.pm.1... 784s parsing sequence Sim.pm.2... 784s Parsed 86 reference bases 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '1' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '2' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '3' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '6' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '9' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '14' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '17' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '24' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '25' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '28' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '30' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '34' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '37' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '38' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '40' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '41' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '42' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '44' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '47' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '50' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '54' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '56' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '59' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: skipping read '60' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '60' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '62' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '70' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 784s Warning: skipping read '72' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '72' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '74' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: skipping read '78' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '78' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 784s Warning: skipping read '79' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '79' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 784s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '82' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 784s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '85' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 784s 87 reads; of these: 784s 87 (100.00%) were unpaired; of these: 784s 73 (83.91%) aligned 0 times 784s 8 (9.20%) aligned exactly 1 time 784s 6 (6.90%) aligned >1 times 784s 16.09% overall alignment rate 784s Read 50 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AAT 784s AAT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATCA 784s ATCA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CCACCCTCTTTC 784s CCACCCTCTTTC 784s Processing line... 784s Processing line... 784s ATG 784s ATG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GA 784s GA 784s Processing line... 784s Processing line... 784s Processing line... 784s CAAT 784s CAAT 784s /usr/bin/bowtie2 --score-min L,2.27334188727385,5.12469200398718 --mm -N 1 -L17 --mp 9.47994892103396,1.52523335844504 --cp-min 5 --cp-ival 2 --trim3 8 -q -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GGGCCA 784s GGGCCA 784s Processing line... 784s Processing line... 784s TGACTGGATCTCA 784s TGACTGGATCTCA 784s Processing line... 784s Processing line... 784s GATCTCAAA 784s GATCTCAAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GCA 784s GCA 784s Processing line... 784s Processing line... 784s Processing line... 784s CAA 784s CAA 784s Processing line... 784s CCACCGGGAG 784s CCACCGGGAG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CGGCCGCCAC 784s CGGCCGCCAC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GTGCAATTCGA 784s GTGCAATTCGA 784s --- Summary --- 784s Read 1 reference strings 784s Checked 14 alignments, 0 edits 784s --------------- 784s PASSED 784s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '1' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '2' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '3' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '6' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: skipping read '9' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '9' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '14' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '17' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: skipping read '24' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '24' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '25' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '28' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: skipping read '30' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '30' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '34' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: skipping read '37' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '37' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '38' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '40' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '41' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: skipping read '42' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '42' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: skipping read '44' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '44' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: skipping read '47' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '47' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '50' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: skipping read '54' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '54' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: skipping read '56' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '56' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: skipping read '59' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '59' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: skipping read '60' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '60' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '62' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: skipping read '70' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '70' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 784s Warning: skipping read '72' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '72' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: skipping read '74' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '74' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: skipping read '78' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '78' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 784s Warning: skipping read '79' because length (1) <= # seed mismatches (1) 784s Warning: skipping read '79' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 784s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '82' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 784s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '85' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 784s 87 reads; of these: 784s 87 (100.00%) were unpaired; of these: 784s 73 (83.91%) aligned 0 times 784s 8 (9.20%) aligned exactly 1 time 784s 6 (6.90%) aligned >1 times 784s 16.09% overall alignment rate 784s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.1 784s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutating sequence Sim.pm.2 784s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 4 784s Reference gaps introduced: 0 784s Read gaps introduced: 0 784s Rearrangements introduced: 1 784s Created read sampler 784s Sampling 119 reads 784s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 784s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 784s parsing sequence Sim.pm.1... 784s parsing sequence Sim.pm.2... 784s Parsed 86 reference bases 784s *** Run 29 of 100 784s /usr/bin/bowtie2 --mm -M 8 --trim5 7 --score-min L,9.94822814203771,5.89875732240936 --cp-min 2 --cp-ival 3 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 784s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '12' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 784s Warning: skipping read '22' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '25' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '27' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '28' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '29' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '40' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 784s Warning: skipping read '41' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '46' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '49' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '54' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '56' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '59' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '60' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '61' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '64' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '67' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '71' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 784s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '81' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 784s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '85' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 784s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '94' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 784s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '99' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 784s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '100' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 784s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '102' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 784s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '114' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 784s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '115' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 784s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '117' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 784s 119 reads; of these: 784s 119 (100.00%) were unpaired; of these: 784s 88 (73.95%) aligned 0 times 784s 16 (13.45%) aligned exactly 1 time 784s 15 (12.61%) aligned >1 times 784s 26.05% overall alignment rate 784s Read 50 alignments... 784s Read 100 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GATCTC 784s GATCTC 784s Processing line... 784s Processing line... 784s Processing line... 784s AGGGCC 784s AGGGCC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AA 784s AA 784s Processing line... 784s Processing line... 784s GCAA 784s GCAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ACT 784s ACT 784s Processing line... 784s TT 784s TT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TCATGACTGGATCTC 784s TCATGACTGGATCTC 784s Processing line... 784s Processing line... 784s Processing line... 784s /usr/bin/bowtie2 --mm -M 8 --trim5 7 --score-min L,9.94822814203771,5.89875732240936 --cp-min 2 --cp-ival 3 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 784s Processing line... 784s TCATGACTGGATCTCA 784s TCATGACTGGATCTCA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AATTCGAATCATGACTGGA 784s AATTCGAATCATGACTGGA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CC 784s CC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CC 784s CC 784s Processing line... 784s TGGA 784s TGGA 784s Processing line... 784s AA 784s AA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATC 784s ATC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TGG 784s TGG 784s Processing line... 784s Processing line... 784s Processing line... 784s TCG 784s TCG 784s Processing line... 784s Processing line... 784s Processing line... 784s TGCAATTCGAATCATGACTGG 784s TGCAATTCGAATCATGACTGG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GCC 784s GCC 784s Processing line... 784s Processing line... 784s CC 784s CC 784s Processing line... 784s TTCGAATCATGACTGGATCTCAA 784s TTCGAATCATGACTGGATCTCAA 784s Processing line... 784s AAG 784s AAG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CAATTCGAATCATGACTGGATCTCAAA 784s CAATTCGAATCATGACTGGATCTCAAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATCG 784s ATCG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATC 784s ATC 784s Processing line... 784s Processing line... 784s TGCAATTCGAATCATGACTGGATCTCAAA 784s TGCAATTCGAATCATGACTGGATCTCAAA 784s Processing line... 784s Processing line... 784s Processing line... 784s CC 784s CC 784s Processing line... 784s Processing line... 784s AACGGCCGCCAC 784s AACGGCCGCCAC 784s Processing line... 784s GCCG 784s GCCG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CCACCGGGAG 784s CCACCGGGAG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATC 784s ATC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TGACTGGATCTCAAAT 784s TGACTGGATCTCAAAT 784s Processing line... 784s --- Summary --- 784s Read 1 reference strings 784s Checked 31 alignments, 0 edits 784s --------------- 784s PASSED 784s ALSO checking that bowtie2 and bowtie2-align match up 784s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '12' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 784s Warning: skipping read '22' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '25' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '27' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '28' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '29' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '40' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 784s Warning: skipping read '41' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '46' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '49' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '54' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '56' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '59' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '60' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '61' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '64' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '67' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '71' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 784s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '81' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 784s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '85' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 784s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '94' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 784s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '99' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 784s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '100' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 784s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '102' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 784s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '114' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 784s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '115' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 784s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '117' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 784s 119 reads; of these: 784s 119 (100.00%) were unpaired; of these: 784s 88 (73.95%) aligned 0 times 784s 16 (13.45%) aligned exactly 1 time 784s 15 (12.61%) aligned >1 times 784s 26.05% overall alignment rate 784s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 784s /usr/bin/bowtie2 --mm -M 8 --trim5 7 --score-min L,9.94822814203771,5.89875732240936 --cp-min 2 --cp-ival 3 -q -p 4 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 784s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 784s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 784s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 784s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '12' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 784s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 784s Warning: skipping read '22' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 784s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '25' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 784s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '27' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 784s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '28' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 784s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '29' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 784s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '40' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 784s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 784s Warning: skipping read '41' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 784s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '46' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 784s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '49' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 784s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '54' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 784s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '56' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '59' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 784s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '60' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '61' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 784s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '64' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 784s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '67' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 784s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '71' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 784s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '81' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 784s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '85' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 784s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '94' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 784s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '99' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 784s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '100' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 784s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '102' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 784s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '114' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 784s Warning: skipping read '115' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '115' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 784s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '117' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 784s 119 reads; of these: 784s 119 (100.00%) were unpaired; of these: 784s 88 (73.95%) aligned 0 times 784s 16 (13.45%) aligned exactly 1 time 784s 15 (12.61%) aligned >1 times 784s 26.05% overall alignment rate 784s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 784s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 784s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.2 784s Introducing 0 SNPs, 0/2 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutating sequence Sim.pm.1 784s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 2 784s Reference gaps introduced: 0 784s Read gaps introduced: 2 784s Rearrangements introduced: 0 784s Created read sampler 784s Sampling 122 reads 784s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 784s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 784s parsing sequence Sim.pm.1... 784s parsing sequence Sim.pm.2... 784s Parsed 86 reference bases 784s *** Run 30 of 100 784s /usr/bin/bowtie2 --score-min L,6.42202429048348,3.41737975342073 --cp-ival 1 -D 13 --local --trim3 1 --np 2 -M 6 --trim5 6 --cp-min 4 -R 1 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 784s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 784s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '1' because it was < 2 characters long 784s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '2' because it was < 2 characters long 784s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '14' because it was < 2 characters long 784s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '15' because it was < 2 characters long 784s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '23' because it was < 2 characters long 784s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '29' because it was < 2 characters long 784s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '33' because it was < 2 characters long 784s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '39' because it was < 2 characters long 784s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '41' because it was < 2 characters long 784s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '54' because it was < 2 characters long 784s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '58' because it was < 2 characters long 784s Warning: skipping read '74' because length (1) <= # seed mismatches (0) 784s Warning: skipping read '74' because it was < 2 characters long 784s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '77' because it was < 2 characters long 784s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '79' because it was < 2 characters long 784s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '87' because it was < 2 characters long 784s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '89' because it was < 2 characters long 784s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '94' because it was < 2 characters long 784s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '99' because it was < 2 characters long 784s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '107' because it was < 2 characters long 784s Warning: skipping read '112' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '112' because it was < 2 characters long 784s Warning: skipping read '117' because length (1) <= # seed mismatches (0) 784s Warning: skipping read '117' because it was < 2 characters long 784s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 784s Warning: skipping read '120' because it was < 2 characters long 784s 122 reads; of these: 784s 122 (100.00%) were unpaired; of these: 784s 122 (100.00%) aligned 0 times 784s 0 (0.00%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 0.00% overall alignment rate 784s Read 50 alignments... 784s Read 100 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s --- Summary --- 784s Read 1 reference strings 784s Checked 0 alignments, 0 edits 784s --------------- 784s PASSED 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.1 784s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutating sequence Sim.pm.2 784s Introducing 8 SNPs, 1/2 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 9 784s Reference gaps introduced: 1 784s Read gaps introduced: 2 784s Rearrangements introduced: 0 784s Created read sampler 784s Sampling 25 reads 784s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 784s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 784s parsing sequence Sim.pm.1... 784s parsing sequence Sim.pm.2... 784s Parsed 86 reference bases 784s *** Run 31 of 100 784s /usr/bin/bowtie2 --rdg 14.7936034772807 --rfg 35.4542817913992 --score-min L,5.68415925658938,7.07071877085189 -i L,0.223263880460258 --trim5 2 --cp-ival 1 --cp-min 8 --mp 8.55828007564592,4.62162041935964 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 784s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '20' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 784s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '23' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 784s 25 reads; of these: 784s 24 (96.00%) were paired; of these: 784s 24 (100.00%) aligned concordantly 0 times 784s 0 (0.00%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 24 pairs aligned concordantly 0 times; of these: 784s 0 (0.00%) aligned discordantly 1 time 784s ---- 784s 24 pairs aligned 0 times concordantly or discordantly; of these: 784s 48 mates make up the pairs; of these: 784s 45 (93.75%) aligned 0 times 784s 2 (4.17%) aligned exactly 1 time 784s 1 (2.08%) aligned >1 times 784s 1 (4.00%) were unpaired; of these: 784s 0 (0.00%) aligned 0 times 784s 1 (100.00%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 8.16% overall alignment rate 784s Read 50 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GGCCA 784s GGCCA 784s Processing line... 784s Processing line... 784s Processing line... 784s AAAG 784s AAAG 784s /usr/bin/bowtie2 --rdg 14.7936034772807 --rfg 35.4542817913992 --score-min L,5.68415925658938,7.07071877085189 -i L,0.223263880460258 --trim5 2 --cp-ival 1 --cp-min 8 --mp 8.55828007564592,4.62162041935964 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TGACTGGATCT 784s TGACTGGATCT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AAGGGCCACCG 784s AAGGGCCACCG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s --- Summary --- 784s Read 1 reference strings 784s Checked 4 alignments, 0 edits 784s --------------- 784s PASSED 784s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 784s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '20' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 784s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '23' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 784s 25 reads; of these: 784s 24 (96.00%) were paired; of these: 784s 24 (100.00%) aligned concordantly 0 times 784s 0 (0.00%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 24 pairs aligned concordantly 0 times; of these: 784s 0 (0.00%) aligned discordantly 1 time 784s ---- 784s 24 pairs aligned 0 times concordantly or discordantly; of these: 784s 48 mates make up the pairs; of these: 784s 45 (93.75%) aligned 0 times 784s 2 (4.17%) aligned exactly 1 time 784s 1 (2.08%) aligned >1 times 784s 1 (4.00%) were unpaired; of these: 784s 0 (0.00%) aligned 0 times 784s 1 (100.00%) aligned exactly 1 time 784s 0 (0.00%) aligned >1 times 784s 8.16% overall alignment rate 784s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.1 784s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutating sequence Sim.pm.2 784s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 2 784s Reference gaps introduced: 0 784s Read gaps introduced: 0 784s Rearrangements introduced: 2 784s Created read sampler 784s Sampling 127 reads 784s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 784s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 784s parsing sequence Sim.pm.1... 784s parsing sequence Sim.pm.2... 784s Parsed 86 reference bases 784s *** Run 32 of 100 784s /usr/bin/bowtie2 --rfg 1.37250007533585 --score-min L,9.1393720525534,3.04605252664279 --trim5 8 -i C,4.26793160744672 -N 1 -L20 --ma 3.73568945961707 --cp-ival 2 --cp-min 5 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 784s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '5' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '14' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 784s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '15' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 784s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '21' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 784s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '34' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 784s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '37' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '39' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 784s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '42' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 784s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '45' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 784s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '53' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 784s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '64' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 784s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '65' because it was < 2 characters long 784s Read 50 alignments... 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 784s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '71' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 784s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '73' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 784s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '79' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 784s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '83' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 784s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '84' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 784s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '85' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 784s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '87' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 784s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '101' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 784s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '103' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 784s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '104' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 784s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '105' because it was < 2 characters long 784s Warning: skipping mate #2 of read '105' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 784s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '113' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 784s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '114' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 784s Warning: skipping mate #2 of read '120' because length (1) <= # seed mismatches (1) 784s Warning: skipping mate #2 of read '120' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 784s Warning: skipping read '123' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '123' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 784s Read 100 alignments... 784s 127 reads; of these: 784s 111 (87.40%) were paired; of these: 784s 111 (100.00%) aligned concordantly 0 times 784s 0 (0.00%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 111 pairs aligned concordantly 0 times; of these: 784s 0 (0.00%) aligned discordantly 1 time 784s ---- 784s 111 pairs aligned 0 times concordantly or discordantly; of these: 784s 222 mates make up the pairs; of these: 784s 195 (87.84%) aligned 0 times 784s 19 (8.56%) aligned exactly 1 time 784s 8 (3.60%) aligned >1 times 784s 16 (12.60%) were unpaired; of these: 784s 12 (75.00%) aligned 0 times 784s 2 (12.50%) aligned exactly 1 time 784s 2 (12.50%) aligned >1 times 784s 13.03% overall alignment rate 784s Read 150 alignments... 784s Read 200 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATTCG 784s ATTCG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATTCGAATCATGACTGGATCTCAAAT 784s ATTCGAATCATGACTGGATCTCAAAT 784s Processing line... 784s Processing line... 784s TGCAATTCGAATCATGACT 784s TGCAATTCGAATCATGACT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AAGGGCCACC 784s AAGGGCCACC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CA 784s CA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s /usr/bin/bowtie2 --rfg 1.37250007533585 --score-min L,9.1393720525534,3.04605252664279 --trim5 8 -i C,4.26793160744672 -N 1 -L20 --ma 3.73568945961707 --cp-ival 2 --cp-min 5 -f -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 784s Processing line... 784s Processing line... 784s Processing line... 784s GTGCAATTCGAA 784s GTGCAATTCGAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GCAATTCGAATCATGACTGGATCTCAAAT 784s GCAATTCGAATCATGACTGGATCTCAAAT 784s Processing line... 784s Processing line... 784s CAAC 784s CAAC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CT 784s CT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GCCACCGGGA 784s GCCACCGGGA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ACC 784s ACC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GCCAC 784s GCCAC 784s Processing line... 784s CCGCCACCCTCTTTCCC 784s CCGCCACCCTCTTTCCC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATCAT 784s ATCAT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CCAAC 784s CCAAC 784s Processing line... 784s Processing line... 784s TTCGAATCATGACTGGATCTCA 784s TTCGAATCATGACTGGATCTCA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TCGAATCATGACTG 784s TCGAATCATGACTG 784s Processing line... 784s CATGACTGGATC 784s CATGACTGGATC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GCA 784s GCA 784s Processing line... 784s Processing line... 784s GCCACCCTCTTTCCC 784s GCCACCCTCTTTCCC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AGGG 784s AGGG 784s Processing line... 784s Processing line... 784s TTCG 784s TTCG 784s Processing line... 784s Processing line... 784s Processing line... 784s GCAATTCGAATCATGACTGGATCTCAAA 784s GCAATTCGAATCATGACTGGATCTCAAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ACGGCCGCCACCCTCTTTCCC 784s ACGGCCGCCACCCTCTTTCCC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AAAGGGCCAC 784s AAAGGGCCAC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CGG 784s CGG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GAT 784s GAT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TGTGCAATTCGAATCATG 784s TGTGCAATTCGAATCATG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CGAATCATGACTGG 784s CGAATCATGACTGG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TGCAATTCGA 784s TGCAATTCGA 784s Processing line... 784s Processing line... 784s TGACT 784s TGACT 784s Processing line... 784s Processing line... 784s Processing line... 784s --- Summary --- 784s Read 1 reference strings 784s Checked 31 alignments, 0 edits 784s --------------- 784s PASSED 784s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 784s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 784s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '5' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 784s Warning: skipping read '14' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '14' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 784s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '15' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 784s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '21' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 784s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '34' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 784s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '37' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 784s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '39' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 784s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '42' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 784s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '45' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 784s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '65' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 784s Warning: skipping mate #1 of read '71' because length (1) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '71' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 784s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '73' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 784s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '79' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 784s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '83' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 784s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '84' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 784s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '85' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 784s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '87' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 784s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '53' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 784s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '64' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 784s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '113' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 784s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '114' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 784s Warning: skipping mate #2 of read '120' because length (1) <= # seed mismatches (1) 784s Warning: skipping mate #2 of read '120' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 784s Warning: skipping read '123' because length (0) <= # seed mismatches (1) 784s Warning: skipping read '123' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 784s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '101' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 784s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '103' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 784s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '104' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 784s Warning: skipping mate #1 of read '105' because length (0) <= # seed mismatches (1) 784s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (1) 784s Warning: skipping mate #1 of read '105' because it was < 2 characters long 784s Warning: skipping mate #2 of read '105' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 784s 127 reads; of these: 784s 111 (87.40%) were paired; of these: 784s 111 (100.00%) aligned concordantly 0 times 784s 0 (0.00%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 111 pairs aligned concordantly 0 times; of these: 784s 0 (0.00%) aligned discordantly 1 time 784s ---- 784s 111 pairs aligned 0 times concordantly or discordantly; of these: 784s 222 mates make up the pairs; of these: 784s 195 (87.84%) aligned 0 times 784s 19 (8.56%) aligned exactly 1 time 784s 8 (3.60%) aligned >1 times 784s 16 (12.60%) were unpaired; of these: 784s 12 (75.00%) aligned 0 times 784s 2 (12.50%) aligned exactly 1 time 784s 2 (12.50%) aligned >1 times 784s 13.03% overall alignment rate 784s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.2 784s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutating sequence Sim.pm.1 784s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 7 784s Reference gaps introduced: 0 784s Read gaps introduced: 0 784s Rearrangements introduced: 0 784s Created read sampler 784s Sampling 113 reads 784s *** Run 33 of 100 784s /usr/bin/bowtie2 --mp 2.96048021951728,1.91437602356168 --nofw --cp-ival 4 --rdg 48.0919217675987 --score-min L,6.12464460106324,7.67390605727305 --mm -a --ma 32.4255276863323 --cp-min 2 -R 4 --np 2 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 784s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 784s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 784s parsing sequence Sim.pm.1... 784s parsing sequence Sim.pm.2... 784s Parsed 86 reference bases 784s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 784s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '23' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 784s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 784s Warning: skipping mate #2 of read '26' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 784s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '36' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 784s Read 50 alignments... 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 784s Read 100 alignments... 784s Read 150 alignments... 784s 113 reads; of these: 784s 113 (100.00%) were paired; of these: 784s 109 (96.46%) aligned concordantly 0 times 784s 4 (3.54%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 109 pairs aligned concordantly 0 times; of these: 784s 1 (0.92%) aligned discordantly 1 time 784s ---- 784s 108 pairs aligned 0 times concordantly or discordantly; of these: 784s 216 mates make up the pairs; of these: 784s 194 (89.81%) aligned 0 times 784s 14 (6.48%) aligned exactly 1 time 784s 8 (3.70%) aligned >1 times 784s 14.16% overall alignment rate 784s Read 200 alignments... 784s Read 250 alignments... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TCGAA 784s TCGAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GG 784s GG 784s Processing line... 784s GG 784s GG 784s Processing line... 784s GG 784s GG 784s Processing line... 784s GG 784s GG 784s Processing line... 784s GG 784s GG 784s Processing line... 784s GG 784s GG 784s Processing line... 784s GG 784s GG 784s Processing line... 784s Processing line... 784s ACTGGATCTCA 784s ACTGGATCTCA 784s Processing line... 784s TTCGAATCATG 784s TTCGAATCATG 784s Processing line... 784s Processing line... 784s Processing line... 784s ATTCGAA 784s ATTCGAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATTC 784s ATTC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AGGC 784s AGGC 784s Processing line... 784s TGTGCAATTCGAATCATGA 784s TGTGCAATTCGAATCATGA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GGAGGC 784s GGAGGC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s /usr/bin/bowtie2 --mp 2.96048021951728,1.91437602356168 --nofw --cp-ival 4 --rdg 48.0919217675987 --score-min L,6.12464460106324,7.67390605727305 --mm -a --ma 32.4255276863323 --cp-min 2 -R 4 --np 2 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 784s Processing line... 784s Processing line... 784s TCAT 784s TCAT 784s Processing line... 784s ATCATGACT 784s ATCATGACT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TCGA 784s TCGA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AGGCAC 784s AGGCAC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATCATGACTGGATCTCA 784s ATCATGACTGGATCTCA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AT 784s AT 784s Processing line... 784s AT 784s AT 784s Processing line... 784s AT 784s AT 784s Processing line... 784s AT 784s AT 784s Processing line... 784s AT 784s AT 784s Processing line... 784s AT 784s AT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AG 784s AG 784s Processing line... 784s AG 784s AG 784s Processing line... 784s Processing line... 784s CG 784s CG 784s Processing line... 784s CG 784s CG 784s Processing line... 784s CG 784s CG 784s Processing line... 784s CG 784s CG 784s Processing line... 784s CG 784s CG 784s Processing line... 784s CG 784s CG 784s Processing line... 784s Processing line... 784s ATCATGACTG 784s ATCATGACTG 784s Processing line... 784s TTCGAATCATGAC 784s TTCGAATCATGAC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GGATCTCA 784s GGATCTCA 784s Processing line... 784s TTCGAA 784s TTCGAA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ACGG 784s ACGG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GA 784s GA 784s Processing line... 784s GA 784s GA 784s Processing line... 784s GA 784s GA 784s Processing line... 784s GA 784s GA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s AAG 784s AAG 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GTGCAATTCGAATCATGACTGGA 784s GTGCAATTCGAATCATGACTGGA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s TTCGAATCATGACTGGATC 784s TTCGAATCATGACTGGATC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GT 784s GT 784s Processing line... 784s Processing line... 784s TCGAATCATGACTGGATCTCA 784s TCGAATCATGACTGGATCTCA 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s GC 784s GC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s CC 784s CC 784s Processing line... 784s CC 784s CC 784s Processing line... 784s CC 784s CC 784s Processing line... 784s CC 784s CC 784s Processing line... 784s CC 784s CC 784s Processing line... 784s CC 784s CC 784s Processing line... 784s CC 784s CC 784s Processing line... 784s CC 784s CC 784s Processing line... 784s CC 784s CC 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s ATT 784s ATT 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s Processing line... 784s --- Summary --- 784s Read 1 reference strings 784s Checked 70 alignments, 0 edits 784s --------------- 784s PASSED 784s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 784s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 784s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '23' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 784s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 784s Warning: skipping mate #2 of read '26' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 784s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 784s Warning: skipping mate #1 of read '36' because it was < 2 characters long 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 784s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 784s 113 reads; of these: 784s 113 (100.00%) were paired; of these: 784s 109 (96.46%) aligned concordantly 0 times 784s 4 (3.54%) aligned concordantly exactly 1 time 784s 0 (0.00%) aligned concordantly >1 times 784s ---- 784s 109 pairs aligned concordantly 0 times; of these: 784s 1 (0.92%) aligned discordantly 1 time 784s ---- 784s 108 pairs aligned 0 times concordantly or discordantly; of these: 784s 216 mates make up the pairs; of these: 784s 194 (89.81%) aligned 0 times 784s 14 (6.48%) aligned exactly 1 time 784s 8 (3.70%) aligned >1 times 784s 14.16% overall alignment rate 784s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 784s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 784s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 784s Flattened IUPAC characters 784s Mutating sequence Sim.pm.2 784s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutating sequence Sim.pm.1 784s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 784s Finished SNPs 784s Finished ref gaps 784s Finished read gaps 784s Mutated reference genome to subject genome 784s SNPs introduced: 3 784s Reference gaps introduced: 0 784s Read gaps introduced: 1 784s Rearrangements introduced: 1 784s Created read sampler 784s Sampling 95 reads 784s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 784s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 784s parsing sequence Sim.pm.1... 785s parsing sequence Sim.pm.2... 785s Parsed 86 reference bases 785s *** Run 34 of 100 785s /usr/bin/bowtie2 --cp-min 2 --np 3 --norc -k 15 --trim5 7 --cp-ival 1 --local --mp 8.73082612320791,3.70645490430699 --trim3 4 --rfg 20.3347579191692,19.5007434727453 --rdg 32.5266111478032 --score-min L,6.87131694101819,8.70683766439613 --mm --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq 785s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 785s 95 reads; of these: 785s 95 (100.00%) were unpaired; of these: 785s 95 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s Read 50 alignments... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s --- Summary --- 785s Read 1 reference strings 785s Checked 0 alignments, 0 edits 785s --------------- 785s PASSED 785s ALSO checking that bowtie2 and bowtie2-align match up 785s /usr/bin/bowtie2 --cp-min 2 --np 3 --norc -k 15 --trim5 7 --cp-ival 1 --local --mp 8.73082612320791,3.70645490430699 --trim3 4 --rfg 20.3347579191692,19.5007434727453 --rdg 32.5266111478032 --score-min L,6.87131694101819,8.70683766439613 --mm --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 785s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (1) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 785s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 785s 95 reads; of these: 785s 95 (100.00%) were unpaired; of these: 785s 95 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 785s Flattened IUPAC characters 785s Mutating sequence Sim.pm.2 785s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutating sequence Sim.pm.1 785s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutated reference genome to subject genome 785s SNPs introduced: 8 785s Reference gaps introduced: 0 785s Read gaps introduced: 0 785s Rearrangements introduced: 0 785s Created read sampler 785s Sampling 12 reads 785s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 785s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 785s *** Run 35 of 100 785s /usr/bin/bowtie2 --cp-min 3 --norc -M 4 --cp-ival 1 --trim3 6 --score-min L,3.54493877539402,5.25388551390742 --gbar 3 --mm -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 785s parsing sequence Sim.pm.1... 785s parsing sequence Sim.pm.2... 785s Parsed 86 reference bases 785s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 785s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '1' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 785s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '2' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 785s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '7' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 785s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '10' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 785s 12 reads; of these: 785s 12 (100.00%) were paired; of these: 785s 12 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 12 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 12 pairs aligned 0 times concordantly or discordantly; of these: 785s 24 mates make up the pairs; of these: 785s 21 (87.50%) aligned 0 times 785s 2 (8.33%) aligned exactly 1 time 785s 1 (4.17%) aligned >1 times 785s 12.50% overall alignment rate 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s CCAC 785s CCAC 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s TGC 785s TGC 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s TGTGCAATTCGAAT 785s TGTGCAATTCGAAT 785s Processing line... 785s Processing line... 785s Processing line... 785s --- Summary --- 785s Read 1 reference strings 785s Checked 3 alignments, 0 edits 785s --------------- 785s PASSED 785s Flattened IUPAC characters 785s Mutating sequence Sim.pm.2 785s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutating sequence Sim.pm.1 785s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutated reference genome to subject genome 785s SNPs introduced: 10 785s Reference gaps introduced: 2 785s Read gaps introduced: 0 785s Rearrangements introduced: 0 785s Created read sampler 785s Sampling 224 reads 785s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 785s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 785s parsing sequence Sim.pm.1... 785s parsing sequence Sim.pm.2... 785s Parsed 86 reference bases 785s *** Run 36 of 100 785s /usr/bin/bowtie2 --score-min L,8.88453153343181,5.27578784266578 --mm -a --cp-ival 2 -D 47 --local --n-ceil 1.00228707035743,0.853595990015035 --cp-min 5 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 785s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '12' because it was < 2 characters long 785s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '18' because it was < 2 characters long 785s Read 50 alignments... 785s Read 100 alignments... 785s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '66' because it was < 2 characters long 785s Warning: skipping mate #1 of read '92' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '92' because it was < 2 characters long 785s Warning: skipping mate #2 of read '141' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '141' because it was < 2 characters long 785s Read 150 alignments... 785s Warning: skipping mate #1 of read '147' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '147' because it was < 2 characters long 785s Warning: skipping mate #2 of read '199' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '199' because it was < 2 characters long 785s Warning: skipping mate #1 of read '201' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '201' because it was < 2 characters long 785s Warning: skipping mate #2 of read '220' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '220' because it was < 2 characters long 785s Read 200 alignments... 785s Read 250 alignments... 785s Read 300 alignments... 785s 224 reads; of these: 785s 224 (100.00%) were paired; of these: 785s 224 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 224 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 224 pairs aligned 0 times concordantly or discordantly; of these: 785s 448 mates make up the pairs; of these: 785s 448 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s Read 350 alignments... 785s Read 400 alignments... 785s Read 450 alignments... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing 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line... 785s /usr/bin/bowtie2 --score-min L,8.88453153343181,5.27578784266578 --mm -a --cp-ival 2 -D 47 --local --n-ceil 1.00228707035743,0.853595990015035 --cp-min 5 -q -p 2 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing 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Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s --- Summary --- 785s Read 1 reference strings 785s Checked 0 alignments, 0 edits 785s --------------- 785s PASSED 785s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 785s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '12' because it was < 2 characters long 785s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '18' because it was < 2 characters long 785s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '66' because it was < 2 characters long 785s Warning: skipping mate #1 of read '92' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '92' because it was < 2 characters long 785s Warning: skipping mate #2 of read '141' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '141' because it was < 2 characters long 785s Warning: skipping mate #1 of read '147' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '147' because it was < 2 characters long 785s Warning: skipping mate #2 of read '199' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '199' because it was < 2 characters long 785s Warning: skipping mate #1 of read '201' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '201' because it was < 2 characters long 785s Warning: skipping mate #2 of read '220' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '220' because it was < 2 characters long 785s 224 reads; of these: 785s 224 (100.00%) were paired; of these: 785s 224 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 224 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 224 pairs aligned 0 times concordantly or discordantly; of these: 785s 448 mates make up the pairs; of these: 785s 448 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 785s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 785s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 785s /usr/bin/bowtie2 --score-min L,8.88453153343181,5.27578784266578 --mm -a --cp-ival 2 -D 47 --local --n-ceil 1.00228707035743,0.853595990015035 --cp-min 5 -q -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 785s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 785s Warning: skipping mate #2 of read '12' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '12' because it was < 2 characters long 785s Warning: skipping mate #1 of read '18' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '18' because it was < 2 characters long 785s Warning: skipping mate #2 of read '66' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '66' because it was < 2 characters long 785s Warning: skipping mate #1 of read '92' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '92' because it was < 2 characters long 785s Warning: skipping mate #2 of read '141' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '141' because it was < 2 characters long 785s Warning: skipping mate #1 of read '147' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '147' because it was < 2 characters long 785s Warning: skipping mate #2 of read '199' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '199' because it was < 2 characters long 785s Warning: skipping mate #1 of read '201' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '201' because it was < 2 characters long 785s Warning: skipping mate #2 of read '220' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '220' because it was < 2 characters long 785s 224 reads; of these: 785s 224 (100.00%) were paired; of these: 785s 224 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 224 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 224 pairs aligned 0 times concordantly or discordantly; of these: 785s 448 mates make up the pairs; of these: 785s 448 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 785s Flattened IUPAC characters 785s Mutating sequence Sim.pm.1 785s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutating sequence Sim.pm.2 785s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutated reference genome to subject genome 785s SNPs introduced: 3 785s Reference gaps introduced: 0 785s Read gaps introduced: 1 785s Rearrangements introduced: 1 785s Created read sampler 785s Sampling 88 reads 785s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 785s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 785s parsing sequence Sim.pm.1... 785s parsing sequence Sim.pm.2... 785s Parsed 86 reference bases 785s *** Run 37 of 100 785s /usr/bin/bowtie2 --score-min L,6.79467439956373,8.10594827682041 --norc -a --mp 9.17351417324911,7.18787766945064 --cp-min 2 --cp-ival 1 --n-ceil 0.553998145083824,0.748988325551156 --local --trim3 3 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 785s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '1' because it was < 2 characters long 785s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '3' because it was < 2 characters long 785s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '9' because it was < 2 characters long 785s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '13' because it was < 2 characters long 785s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '17' because it was < 2 characters long 785s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '33' because it was < 2 characters long 785s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '36' because it was < 2 characters long 785s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '57' because it was < 2 characters long 785s Read 50 alignments... 785s Read 100 alignments... 785s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '72' because it was < 2 characters long 785s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '82' because it was < 2 characters long 785s 88 reads; of these: 785s 82 (93.18%) were paired; of these: 785s 82 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 82 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 82 pairs aligned 0 times concordantly or discordantly; of these: 785s 164 mates make up the pairs; of these: 785s 164 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 6 (6.82%) were unpaired; of these: 785s 6 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s Read 150 alignments... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s --- Summary --- 785s Read 1 reference strings 785s Checked 0 alignments, 0 edits 785s --------------- 785s PASSED 785s ALSO checking that bowtie2 and bowtie2-align match up 785s /usr/bin/bowtie2 --score-min L,6.79467439956373,8.10594827682041 --norc -a --mp 9.17351417324911,7.18787766945064 --cp-min 2 --cp-ival 1 --n-ceil 0.553998145083824,0.748988325551156 --local --trim3 3 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 785s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '1' because it was < 2 characters long 785s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '3' because it was < 2 characters long 785s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '9' because it was < 2 characters long 785s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '13' because it was < 2 characters long 785s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '17' because it was < 2 characters long 785s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '33' because it was < 2 characters long 785s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '36' because it was < 2 characters long 785s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '57' because it was < 2 characters long 785s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '72' because it was < 2 characters long 785s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '82' because it was < 2 characters long 785s 88 reads; of these: 785s 82 (93.18%) were paired; of these: 785s 82 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 82 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 82 pairs aligned 0 times concordantly or discordantly; of these: 785s 164 mates make up the pairs; of these: 785s 164 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 6 (6.82%) were unpaired; of these: 785s 6 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 785s Flattened IUPAC characters 785s Mutating sequence Sim.pm.1 785s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutating sequence Sim.pm.2 785s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutated reference genome to subject genome 785s SNPs introduced: 4 785s Reference gaps introduced: 0 785s Read gaps introduced: 0 785s Rearrangements introduced: 1 785s Created read sampler 785s Sampling 44 reads 785s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 785s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 785s parsing sequence Sim.pm.1... 785s parsing sequence Sim.pm.2... 785s Parsed 86 reference bases 785s *** Run 38 of 100 785s /usr/bin/bowtie2 --cp-min 3 --ma 34.1134201798778 -R 2 --np 2 --trim5 4 --cp-ival 1 --n-ceil 0.509615057295784,1.44673701467581 --trim3 5 --score-min L,3.84329634796837,5.61194162257716 --rfg 10.8457721322266 -a -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 785s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 785s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 785s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '5' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 785s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '9' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 785s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '11' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 785s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '12' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 785s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '16' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 785s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '20' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 785s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '31' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 785s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '37' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 785s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '39' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 785s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '40' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 785s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '41' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 785s 44 reads; of these: 785s 44 (100.00%) were unpaired; of these: 785s 34 (77.27%) aligned 0 times 785s 5 (11.36%) aligned exactly 1 time 785s 5 (11.36%) aligned >1 times 785s 22.73% overall alignment rate 785s Read 50 alignments... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s TTCGAATCATGACTGG 785s TTCGAATCATGACTGG 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s CCAACGGCCGCCACCCTCT 785s CCAACGGCCGCCACCCTCT 785s Processing line... 785s Processing line... 785s CC 785s CC 785s Processing line... 785s CC 785s CC 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s GG 785s GG 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s CC 785s CC 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s Processing line... 785s Processing line... 785s CTGGATC 785s CTGGATC 785s Processing line... 785s Processing line... 785s Processing line... 785s GCCAC 785s GCCAC 785s Processing line... 785s GCCAC 785s GCCAC 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s GCAATTCGAATCATGACTGGATCTCA 785s GCAATTCGAATCATGACTGGATCTCA 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s CC 785s CC 785s Processing line... 785s CC 785s CC 785s Processing line... 785s CC 785s CC 785s Processing line... 785s CC 785s CC 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s GG 785s GG 785s Processing line... 785s GG 785s GG 785s Processing line... 785s CC 785s CC 785s Processing line... 785s GG 785s GG 785s Processing line... 785s GG 785s GG 785s Processing line... 785s GG 785s GG 785s Processing line... 785s CC 785s CC 785s Processing line... 785s CC 785s CC 785s Processing line... 785s Processing line... 785s ACTGGATCT 785s ACTGGATCT 785s Processing line... 785s GCA 785s GCA 785s Processing line... 785s GCA 785s GCA 785s Processing line... 785s TGC 785s TGC 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s CGAA 785s CGAA 785s Processing line... 785s TTCG 785s TTCG 785s --- Summary --- 785s Read 1 reference strings 785s Checked 44 alignments, 0 edits 785s --------------- 785s PASSED 785s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 785s /usr/bin/bowtie2 --cp-min 3 --ma 34.1134201798778 -R 2 --np 2 --trim5 4 --cp-ival 1 --n-ceil 0.509615057295784,1.44673701467581 --trim3 5 --score-min L,3.84329634796837,5.61194162257716 --rfg 10.8457721322266 -a -f -p 3 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 785s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 785s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 785s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '5' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 785s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '9' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 785s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '11' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 785s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '12' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 785s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '16' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 785s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '20' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 785s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '31' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 785s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '37' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 785s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '39' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 785s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '40' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 785s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '41' because it was < 2 characters long 785s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 785s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 785s 44 reads; of these: 785s 44 (100.00%) were unpaired; of these: 785s 34 (77.27%) aligned 0 times 785s 5 (11.36%) aligned exactly 1 time 785s 5 (11.36%) aligned >1 times 785s 22.73% overall alignment rate 785s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 785s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 785s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 785s Flattened IUPAC characters 785s Mutating sequence Sim.pm.2 785s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutating sequence Sim.pm.1 785s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutated reference genome to subject genome 785s SNPs introduced: 2 785s Reference gaps introduced: 1 785s Read gaps introduced: 0 785s Rearrangements introduced: 2 785s Created read sampler 785s Sampling 128 reads 785s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 785s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 785s parsing sequence Sim.pm.1... 785s parsing sequence Sim.pm.2... 785s Parsed 86 reference bases 785s *** Run 39 of 100 785s /usr/bin/bowtie2 -D 16 --cp-ival 2 --local --trim3 2 --gbar 2 --rdg 27.3145837256404 --rfg 12.5030784698956,15.2208031489366 --score-min L,7.743946516996,8.3031623041112 -a --cp-min 6 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 785s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '14' because it was < 2 characters long 785s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '17' because it was < 2 characters long 785s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '20' because it was < 2 characters long 785s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '29' because it was < 2 characters long 785s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '42' because it was < 2 characters long 785s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '45' because it was < 2 characters long 785s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '47' because it was < 2 characters long 785s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '55' because it was < 2 characters long 785s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '64' because it was < 2 characters long 785s Read 50 alignments... 785s Read 100 alignments... 785s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '67' because it was < 2 characters long 785s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '77' because it was < 2 characters long 785s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '97' because it was < 2 characters long 785s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '98' because it was < 2 characters long 785s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '110' because it was < 2 characters long 785s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '116' because it was < 2 characters long 785s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '125' because it was < 2 characters long 785s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '126' because it was < 2 characters long 785s 128 reads; of these: 785s 120 (93.75%) were paired; of these: 785s 120 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 120 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 120 pairs aligned 0 times concordantly or discordantly; of these: 785s 240 mates make up the pairs; of these: 785s 240 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 8 (6.25%) were unpaired; of these: 785s 8 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s Read 150 alignments... 785s Read 200 alignments... 785s Read 250 alignments... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s 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line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s Processing line... 785s --- Summary --- 785s Read 1 reference strings 785s Checked 0 alignments, 0 edits 785s --------------- 785s PASSED 785s ALSO checking that bowtie2 and bowtie2-align match up 785s /usr/bin/bowtie2 -D 16 --cp-ival 2 --local --trim3 2 --gbar 2 --rdg 27.3145837256404 --rfg 12.5030784698956,15.2208031489366 --score-min L,7.743946516996,8.3031623041112 -a --cp-min 6 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 785s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '14' because it was < 2 characters long 785s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '17' because it was < 2 characters long 785s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '20' because it was < 2 characters long 785s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '29' because it was < 2 characters long 785s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '42' because it was < 2 characters long 785s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '45' because it was < 2 characters long 785s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '47' because it was < 2 characters long 785s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '55' because it was < 2 characters long 785s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '64' because it was < 2 characters long 785s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '67' because it was < 2 characters long 785s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '77' because it was < 2 characters long 785s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '97' because it was < 2 characters long 785s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '98' because it was < 2 characters long 785s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '110' because it was < 2 characters long 785s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '116' because it was < 2 characters long 785s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '125' because it was < 2 characters long 785s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '126' because it was < 2 characters long 785s 128 reads; of these: 785s 120 (93.75%) were paired; of these: 785s 120 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 120 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 120 pairs aligned 0 times concordantly or discordantly; of these: 785s 240 mates make up the pairs; of these: 785s 240 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 8 (6.25%) were unpaired; of these: 785s 8 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 785s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 785s /usr/bin/bowtie2 -D 16 --cp-ival 2 --local --trim3 2 --gbar 2 --rdg 27.3145837256404 --rfg 12.5030784698956,15.2208031489366 --score-min L,7.743946516996,8.3031623041112 -a --cp-min 6 -q -p 3 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 785s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '14' because it was < 2 characters long 785s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '17' because it was < 2 characters long 785s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '20' because it was < 2 characters long 785s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '29' because it was < 2 characters long 785s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '42' because it was < 2 characters long 785s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '45' because it was < 2 characters long 785s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '47' because it was < 2 characters long 785s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '55' because it was < 2 characters long 785s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '64' because it was < 2 characters long 785s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '67' because it was < 2 characters long 785s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '77' because it was < 2 characters long 785s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '97' because it was < 2 characters long 785s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '98' because it was < 2 characters long 785s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '110' because it was < 2 characters long 785s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '116' because it was < 2 characters long 785s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '125' because it was < 2 characters long 785s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '126' because it was < 2 characters long 785s 128 reads; of these: 785s 120 (93.75%) were paired; of these: 785s 120 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 120 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 120 pairs aligned 0 times concordantly or discordantly; of these: 785s 240 mates make up the pairs; of these: 785s 240 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 8 (6.25%) were unpaired; of these: 785s 8 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 785s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 785s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 785s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 785s /usr/bin/bowtie2 -D 16 --cp-ival 2 --local --trim3 2 --gbar 2 --rdg 27.3145837256404 --rfg 12.5030784698956,15.2208031489366 --score-min L,7.743946516996,8.3031623041112 -a --cp-min 6 -q -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 785s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '14' because it was < 2 characters long 785s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '17' because it was < 2 characters long 785s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '20' because it was < 2 characters long 785s Warning: skipping mate #2 of read '29' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '29' because it was < 2 characters long 785s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '42' because it was < 2 characters long 785s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '45' because it was < 2 characters long 785s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '47' because it was < 2 characters long 785s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '55' because it was < 2 characters long 785s Warning: skipping mate #2 of read '64' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '64' because it was < 2 characters long 785s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '67' because it was < 2 characters long 785s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '77' because it was < 2 characters long 785s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 785s Warning: skipping mate #2 of read '97' because it was < 2 characters long 785s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '98' because it was < 2 characters long 785s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '110' because it was < 2 characters long 785s Warning: skipping mate #1 of read '116' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '116' because it was < 2 characters long 785s Warning: skipping read '125' because length (0) <= # seed mismatches (0) 785s Warning: skipping read '125' because it was < 2 characters long 785s Warning: skipping mate #1 of read '126' because length (0) <= # seed mismatches (0) 785s Warning: skipping mate #1 of read '126' because it was < 2 characters long 785s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 785s 128 reads; of these: 785s 120 (93.75%) were paired; of these: 785s 120 (100.00%) aligned concordantly 0 times 785s 0 (0.00%) aligned concordantly exactly 1 time 785s 0 (0.00%) aligned concordantly >1 times 785s ---- 785s 120 pairs aligned concordantly 0 times; of these: 785s 0 (0.00%) aligned discordantly 1 time 785s ---- 785s 120 pairs aligned 0 times concordantly or discordantly; of these: 785s 240 mates make up the pairs; of these: 785s 240 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 8 (6.25%) were unpaired; of these: 785s 8 (100.00%) aligned 0 times 785s 0 (0.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 0.00% overall alignment rate 785s Flattened IUPAC characters 785s Mutating sequence Sim.pm.1 785s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutating sequence Sim.pm.2 785s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 785s Finished SNPs 785s Finished ref gaps 785s Finished read gaps 785s Mutated reference genome to subject genome 785s SNPs introduced: 1 785s Reference gaps introduced: 1 785s Read gaps introduced: 0 785s Rearrangements introduced: 1 785s Created read sampler 785s Sampling 74 reads 785s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 785s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 785s *** Run 40 of 100 785s /usr/bin/bowtie2 --mp 6.1834867664596,3.32976840577569 -N 1 -L21 --cp-ival 1 --trim3 7 --score-min L,7.71151933375706,6.41610737907194 --rfg 30.1046326118027 --mm --ma 35.066292562352 --cp-min 4 -R 2 --norc --np 6 -i L,0.111878272150482 --trim5 3 -k 3 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 785s parsing sequence Sim.pm.1... 785s parsing sequence Sim.pm.2... 785s Parsed 86 reference bases 786s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 786s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 786s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 786s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '3' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 786s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '7' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 786s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '8' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 786s Warning: skipping read '10' because length (0) <= # seed mismatches (1) 786s Warning: skipping read '10' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 786s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '14' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 786s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '19' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 786s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '27' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 786s Warning: skipping read '31' because length (0) <= # seed mismatches (1) 786s Warning: skipping read '31' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 786s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '34' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 786s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '38' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 786s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '41' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 786s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '42' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 786s Warning: skipping mate #1 of read '44' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '44' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 786s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '49' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 786s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '62' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 786s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '66' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 786s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '67' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 786s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '68' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 786s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '69' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 786s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read '72' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 786s 74 reads; of these: 786s 58 (78.38%) were paired; of these: 786s 56 (96.55%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 2 (3.45%) aligned concordantly >1 times 786s ---- 786s 56 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 56 pairs aligned 0 times concordantly or discordantly; of these: 786s 112 mates make up the pairs; of these: 786s 104 (92.86%) aligned 0 times 786s 6 (5.36%) aligned exactly 1 time 786s 2 (1.79%) aligned >1 times 786s 16 (21.62%) were unpaired; of these: 786s 14 (87.50%) aligned 0 times 786s 2 (12.50%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 10.61% overall alignment rate 786s Read 50 alignments... 786s Read 100 alignments... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AATC 786s AATC 786s Processing line... 786s AATC 786s AATC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GGGCC 786s GGGCC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s TTCGAA 786s TTCGAA 786s Processing line... 786s CCG 786s CCG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AA 786s AA 786s Processing line... 786s AA 786s AA 786s Processing line... 786s AA 786s AA 786s Processing line... 786s Processing line... 786s Processing line... 786s TTCGAATCATGACTGGATCTCAA 786s TTCGAATCATGACTGGATCTCAA 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GTGCAATTCGAATCAT 786s GTGCAATTCGAATCAT 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s ATCTCAAA 786s ATCTCAAA 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GGCCACC 786s GGCCACC 786s Processing line... 786s Processing line... 786s TCGA 786s TCGA 786s Processing line... 786s TCA 786s TCA 786s Processing line... 786s TCGA 786s TCGA 786s Processing line... 786s TCA 786s TCA 786s Processing line... 786s TTCGAAT 786s TTCGAAT 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GACTGGATCTCAAAT 786s GACTGGATCTCAAAT 786s Processing line... 786s GCCACCGG 786s GCCACCGG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s --- Summary --- 786s Read 1 reference strings 786s Checked 19 alignments, 0 edits 786s --------------- 786s PASSED 786s Flattened IUPAC characters 786s Mutating sequence Sim.pm.1 786s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutating sequence Sim.pm.2 786s Introducing 0 SNPs, 2/2 ref/read gaps, and 1 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutated reference genome to subject genome 786s SNPs introduced: 1 786s Reference gaps introduced: 2 786s Read gaps introduced: 3 786s Rearrangements introduced: 1 786s Created read sampler 786s Sampling 161 reads 786s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 786s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 786s parsing sequence Sim.pm.1... 786s *** Run 41 of 100 786s /usr/bin/bowtie2 --score-min L,9.58388887468286,3.77858249991178 -M 2 --trim5 8 --mm --cp-min 5 --cp-ival 4 --nofw --ma 21.4854809996979 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 786s parsing sequence Sim.pm.2... 786s Parsed 86 reference bases 786s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 786s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 786s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 786s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '3' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 786s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '5' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 786s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '6' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 786s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '9' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 786s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '10' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 786s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '11' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 786s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '12' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 786s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '17' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 786s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 786s Warning: skipping read '20' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 786s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '30' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 786s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '31' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 786s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '34' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 786s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '35' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 786s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '37' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 786s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '38' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 786s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '40' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 786s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '42' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 786s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '45' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 786s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '49' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 786s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '53' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 786s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 786s Warning: skipping read '54' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 786s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '56' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 786s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '67' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 786s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '68' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 786s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '71' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 786s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '72' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 786s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '73' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 786s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '74' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 786s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '80' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 786s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '84' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 786s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '85' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 786s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '86' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 786s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '93' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 786s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '97' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 786s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '100' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 786s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '105' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 786s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '110' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 786s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '114' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 786s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '116' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 786s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '127' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 786s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '129' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 786s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '136' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 786s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '142' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 786s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '153' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 786s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '154' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 786s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '155' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 786s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '159' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 786s 161 reads; of these: 786s 161 (100.00%) were unpaired; of these: 786s 142 (88.20%) aligned 0 times 786s 13 (8.07%) aligned exactly 1 time 786s 6 (3.73%) aligned >1 times 786s 11.80% overall alignment rate 786s Read 50 alignments... 786s Read 100 alignments... 786s Read 150 alignments... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AC 786s AC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s TCCCGC 786s TCCCGC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GTGCAATTCGAATCA 786s GTGCAATTCGAATCA 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AC 786s AC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GACTGGATCTCAA 786s GACTGGATCTCAA 786s Processing line... 786s Processing line... 786s Processing line... 786s CTTTCCCGC 786s CTTTCCCGC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s CAACGGCCG 786s CAACGGCCG 786s /usr/bin/bowtie2 --score-min L,9.58388887468286,3.77858249991178 -M 2 --trim5 8 --mm --cp-min 5 --cp-ival 4 --nofw --ma 21.4854809996979 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 786s Processing line... 786s Processing line... 786s GGATCT 786s GGATCT 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GGGAGGC 786s GGGAGGC 786s Processing line... 786s CGG 786s CGG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GGATCT 786s GGATCT 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s ACTGGAT 786s ACTGGAT 786s Processing line... 786s GGC 786s GGC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s CTT 786s CTT 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s TTCGAATCATG 786s TTCGAATCATG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s ATTCGAATCATGAC 786s ATTCGAATCATGAC 786s Processing line... 786s TCG 786s TCG 786s Processing line... 786s Processing line... 786s CCA 786s CCA 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GTGCAATTC 786s GTGCAATTC 786s Processing line... 786s --- Summary --- 786s Read 1 reference strings 786s Checked 19 alignments, 0 edits 786s --------------- 786s PASSED 786s ALSO checking that bowtie2 and bowtie2-align match up 786s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 786s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 786s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 786s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '3' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 786s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '5' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 786s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '6' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 786s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '9' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 786s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '10' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 786s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '11' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 786s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '12' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 786s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '17' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 786s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 786s Warning: skipping read '20' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 786s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '30' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 786s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '31' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 786s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '34' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 786s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '35' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 786s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '37' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 786s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '38' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 786s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '40' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 786s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '42' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 786s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '45' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 786s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '49' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 786s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '53' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 786s Warning: skipping read '54' because length (1) <= # seed mismatches (0) 786s Warning: skipping read '54' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 786s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '56' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 786s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '67' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 786s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '68' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 786s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '71' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 786s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '72' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 786s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '73' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 786s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '74' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 786s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '80' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 786s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '84' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 786s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '85' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 786s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '86' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 786s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '93' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 786s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '97' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 786s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '100' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 786s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '105' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 786s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '110' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 786s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '114' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 786s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '116' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 786s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '127' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 786s Warning: skipping read '129' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '129' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 786s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '136' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 786s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '142' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 786s Warning: skipping read '153' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '153' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 786s Warning: skipping read '154' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '154' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 786s Warning: skipping read '155' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '155' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 786s Warning: skipping read '159' because length (0) <= # seed mismatches (0) 786s Warning: skipping read '159' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 786s 161 reads; of these: 786s 161 (100.00%) were unpaired; of these: 786s 142 (88.20%) aligned 0 times 786s 13 (8.07%) aligned exactly 1 time 786s 6 (3.73%) aligned >1 times 786s 11.80% overall alignment rate 786s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 786s Flattened IUPAC characters 786s Mutating sequence Sim.pm.2 786s Introducing 0 SNPs, 2/1 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutating sequence Sim.pm.1 786s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutated reference genome to subject genome 786s SNPs introduced: 0 786s Reference gaps introduced: 2 786s Read gaps introduced: 1 786s Rearrangements introduced: 0 786s Created read sampler 786s Sampling 34 reads 786s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 786s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 786s parsing sequence Sim.pm.1... 786s parsing sequence Sim.pm.2... 786s Parsed 86 reference bases 786s *** Run 42 of 100 786s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 1.32840898023674,0.432565482923792 --cp-min 9 --mp 3.97643290646225,2.95201744740898 --ma 23.9228090226831 --gbar 2 --score-min L,7.09180650012733,9.22527001758477 --trim5 6 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 786s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 786s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 786s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 786s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 786s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 786s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 786s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 786s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 786s Warning: skipping mate #2 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 786s 34 reads; of these: 786s 31 (91.18%) were paired; of these: 786s 31 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 31 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 31 pairs aligned 0 times concordantly or discordantly; of these: 786s 62 mates make up the pairs; of these: 786s 52 (83.87%) aligned 0 times 786s 9 (14.52%) aligned exactly 1 time 786s 1 (1.61%) aligned >1 times 786s 3 (8.82%) were unpaired; of these: 786s 3 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 15.38% overall alignment rate 786s Read 50 alignments... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s ATGACTGGATCTCAAAT 786s ATGACTGGATCTCAAAT 786s Processing line... 786s Processing line... 786s CCACCG 786s CCACCG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s CAAC 786s CAAC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s ATTCGAATCATG 786s ATTCGAATCATG 786s Processing line... 786s Processing line... 786s ACTGGATC 786s ACTGGATC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AATCATGACTGG 786s AATCATGACTGG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AA 786s AA 786s Processing line... 786s Processing line... 786s CAACGGCCGCCACCCT 786s CAACGGCCGCCACCCT 786s Processing line... 786s Processing line... 786s ATCATGACTGGATCTCAAA 786s ATCATGACTGGATCTCAAA 786s Processing line... 786s Processing line... 786s GACTGGATC 786s GACTGGATC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s --- Summary --- 786s Read 1 reference strings 786s Checked 10 alignments, 0 edits 786s --------------- 786s PASSED 786s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 786s /usr/bin/bowtie2 --cp-ival 1 --n-ceil 1.32840898023674,0.432565482923792 --cp-min 9 --mp 3.97643290646225,2.95201744740898 --ma 23.9228090226831 --gbar 2 --score-min L,7.09180650012733,9.22527001758477 --trim5 6 --qseq -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 786s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 786s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 786s Warning: skipping read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 786s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 786s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 786s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 786s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 786s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 786s Warning: skipping mate #2 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 786s 34 reads; of these: 786s 31 (91.18%) were paired; of these: 786s 31 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 31 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 31 pairs aligned 0 times concordantly or discordantly; of these: 786s 62 mates make up the pairs; of these: 786s 52 (83.87%) aligned 0 times 786s 9 (14.52%) aligned exactly 1 time 786s 1 (1.61%) aligned >1 times 786s 3 (8.82%) were unpaired; of these: 786s 3 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 15.38% overall alignment rate 786s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 786s Flattened IUPAC characters 786s Mutating sequence Sim.pm.2 786s Introducing 4 SNPs, 2/2 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutating sequence Sim.pm.1 786s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutated reference genome to subject genome 786s SNPs introduced: 7 786s Reference gaps introduced: 2 786s Read gaps introduced: 3 786s Rearrangements introduced: 0 786s Created read sampler 786s Sampling 90 reads 786s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 786s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 786s parsing sequence Sim.pm.1... 786s parsing sequence Sim.pm.2... 786s Parsed 86 reference bases 786s *** Run 43 of 100 786s /usr/bin/bowtie2 -N 0 -L28 --local --cp-ival 1 --cp-min 2 --trim5 9 --mm --score-min L,5.40007816115704,2.82099780989104 --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq 786s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (1) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 786s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 786s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 786s 90 reads; of these: 786s 90 (100.00%) were unpaired; of these: 786s 90 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 0.00% overall alignment rate 786s Read 50 alignments... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s --- Summary --- 786s Read 1 reference strings 786s Checked 0 alignments, 0 edits 786s --------------- 786s PASSED 786s Flattened IUPAC characters 786s Mutating sequence Sim.pm.1 786s Introducing 4 SNPs, 0/1 ref/read gaps, and 1 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutating sequence Sim.pm.2 786s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutated reference genome to subject genome 786s SNPs introduced: 9 786s Reference gaps introduced: 0 786s Read gaps introduced: 1 786s Rearrangements introduced: 1 786s Created read sampler 786s Sampling 171 reads 786s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 786s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 786s parsing sequence Sim.pm.1... 786s parsing sequence Sim.pm.2... 786s Parsed 86 reference bases 786s *** Run 44 of 100 786s /usr/bin/bowtie2 -N 1 -L26 --mp 6.01304837787017,1.02596631143574 --cp-ival 1 --local -D 7 --score-min L,2.79645957783752,3.76071764187003 --cp-min 2 -i S,0.695827097233992 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 786s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 786s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 786s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 786s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 786s Read 50 alignments... 786s Warning: skipping mate #2 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #2 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 786s Warning: skipping mate #2 of read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #2 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 786s Read 100 alignments... 786s Read 150 alignments... 786s Warning: skipping mate #2 of read 'R_1_1_1_167_167_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #2 of read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 786s Read 200 alignments... 786s 171 reads; of these: 786s 171 (100.00%) were paired; of these: 786s 171 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 171 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 171 pairs aligned 0 times concordantly or discordantly; of these: 786s 342 mates make up the pairs; of these: 786s 342 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 0.00% overall alignment rate 786s Read 250 alignments... 786s Read 300 alignments... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing 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Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s --- Summary --- 786s Read 1 reference strings 786s Checked 0 alignments, 0 edits 786s --------------- 786s PASSED 786s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 786s /usr/bin/bowtie2 -N 1 -L26 --mp 6.01304837787017,1.02596631143574 --cp-ival 1 --local -D 7 --score-min L,2.79645957783752,3.76071764187003 --cp-min 2 -i S,0.695827097233992 --qseq -p 3 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 786s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 786s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #2 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 786s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 786s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 786s Warning: skipping mate #2 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #2 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 786s Warning: skipping mate #2 of read 'R_1_1_1_135_135_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #2 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 786s Warning: skipping mate #2 of read 'R_1_1_1_167_167_1/1' because length (1) <= # seed mismatches (1) 786s Warning: skipping mate #2 of read 'R_1_1_1_167_167_1/1' because it was < 2 characters long 786s 171 reads; of these: 786s 171 (100.00%) were paired; of these: 786s 171 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 171 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 171 pairs aligned 0 times concordantly or discordantly; of these: 786s 342 mates make up the pairs; of these: 786s 342 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 0.00% overall alignment rate 786s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 786s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 786s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 786s Flattened IUPAC characters 786s Mutating sequence Sim.pm.1 786s Introducing 5 SNPs, 1/1 ref/read gaps, and 1 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutating sequence Sim.pm.2 786s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutated reference genome to subject genome 786s SNPs introduced: 8 786s Reference gaps introduced: 1 786s Read gaps introduced: 1 786s Rearrangements introduced: 1 786s Created read sampler 786s Sampling 135 reads 786s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 786s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 786s parsing sequence Sim.pm.1... 786s *** Run 45 of 100 786s /usr/bin/bowtie2 --score-min L,1.92418047858185,2.40989325840069 --np 2 --mm --ma 20.1694160990419 --cp-ival 1 --n-ceil 0.778982060595171,0.10121709089887 --cp-min 2 --trim3 0 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 786s parsing sequence Sim.pm.2... 786s Parsed 86 reference bases 786s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 786s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '6' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 786s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '17' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 786s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '42' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 786s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '49' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 786s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '58' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 786s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '78' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 786s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '99' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 786s Warning: skipping mate #2 of read '125' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '125' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 786s 135 reads; of these: 786s 135 (100.00%) were paired; of these: 786s 135 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 135 pairs aligned concordantly 0 times; of these: 786s 1 (0.74%) aligned discordantly 1 time 786s ---- 786s 134 pairs aligned 0 times concordantly or discordantly; of these: 786s 268 mates make up the pairs; of these: 786s 230 (85.82%) aligned 0 times 786s 29 (10.82%) aligned exactly 1 time 786s 9 (3.36%) aligned >1 times 786s 14.81% overall alignment rate 786s Read 50 alignments... 786s Read 100 alignments... 786s Read 150 alignments... 786s Read 200 alignments... 786s Read 250 alignments... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GGGCCACCGGGAGGCAC 786s GGGCCACCGGGAGGCAC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s ACTGGATCTC 786s ACTGGATCTC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s CGAATCATGACT 786s CGAATCATGACT 786s Processing line... 786s Processing line... 786s CACCGGGAGGC 786s CACCGGGAGGC 786s Processing line... 786s Processing line... 786s GGAG 786s GGAG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AC 786s AC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s TC 786s TC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AAAGGGCCAC 786s AAAGGGCCAC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s CATGAC 786s CATGAC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GA 786s GA 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s TGCAATTCGA 786s TGCAATTCGA 786s Processing line... 786s Processing line... 786s TGCAATTCGAATC 786s TGCAATTCGAATC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GAATCATGACTGGATCT 786s GAATCATGACTGGATCT 786s Processing line... 786s CCAA 786s CCAA 786s Processing line... 786s TGGA 786s TGGA 786s Processing line... 786s Processing line... 786s AAAGGGCCACCGGGAGGCA 786s AAAGGGCCACCGGGAGGCA 786s Processing line... 786s Processing line... 786s CAATTCGAATCATGACTGGATCTC 786s CAATTCGAATCATGACTGGATCTC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s TC 786s TC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s TCTCAAA 786s TCTCAAA 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s CGGGAG 786s CGGGAG 786s Processing line... 786s Processing line... 786s TTCGAATCA 786s TTCGAATCA 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GAGGCA 786s GAGGCA 786s Processing line... 786s Processing line... 786s AAAGGGCCACCGGGAG 786s AAAGGGCCACCGGGAG 786s Processing line... 786s Processing line... 786s TGTGCAAT 786s TGTGCAAT 786s Processing line... 786s Processing line... 786s GGATCT 786s GGATCT 786s Processing line... 786s Processing line... 786s GCCACCGGGAGGC 786s GCCACCGGGAGGC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s TC 786s TC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s CA 786s CA 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s AAGGG 786s AAGGG 786s Processing line... 786s Processing line... 786s GTGCAATTCGAATCATG 786s GTGCAATTCGAATCATG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s CTGGATCTC 786s CTGGATCTC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GGAG 786s GGAG 786s Processing line... 786s Processing line... 786s AAGGGCCACCGGG 786s AAGGGCCACCGGG 786s Processing line... 786s Processing line... 786s CCT 786s CCT 786s Processing line... 786s TGTGC 786s TGTGC 786s Processing line... 786s GAG 786s GAG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GGAGGCA 786s GGAGGCA 786s Processing line... 786s Processing line... 786s TTTC 786s TTTC 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GGGCCACCGGGAG 786s GGGCCACCGGGAG 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s GT 786s GT 786s Processing line... 786s Processing line... 786s Processing line... 786s --- Summary --- 786s Read 1 reference strings 786s Checked 40 alignments, 0 edits 786s --------------- 786s PASSED 786s ALSO checking that bowtie2 and bowtie2-align match up 786s /usr/bin/bowtie2 --score-min L,1.92418047858185,2.40989325840069 --np 2 --mm --ma 20.1694160990419 --cp-ival 1 --n-ceil 0.778982060595171,0.10121709089887 --cp-min 2 --trim3 0 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 786s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 786s Warning: skipping mate #1 of read '6' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '6' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 786s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '17' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 786s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '42' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 786s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '49' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 786s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '58' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 786s Warning: skipping mate #1 of read '78' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '78' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 786s Warning: skipping mate #2 of read '99' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '99' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 786s Warning: skipping mate #2 of read '125' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '125' because it was < 2 characters long 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 786s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 786s 135 reads; of these: 786s 135 (100.00%) were paired; of these: 786s 135 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 135 pairs aligned concordantly 0 times; of these: 786s 1 (0.74%) aligned discordantly 1 time 786s ---- 786s 134 pairs aligned 0 times concordantly or discordantly; of these: 786s 268 mates make up the pairs; of these: 786s 230 (85.82%) aligned 0 times 786s 29 (10.82%) aligned exactly 1 time 786s 9 (3.36%) aligned >1 times 786s 14.81% overall alignment rate 786s Flattened IUPAC characters 786s Mutating sequence Sim.pm.1 786s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutating sequence Sim.pm.2 786s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutated reference genome to subject genome 786s SNPs introduced: 4 786s Reference gaps introduced: 0 786s Read gaps introduced: 0 786s Rearrangements introduced: 2 786s Created read sampler 786s Sampling 17 reads 786s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 786s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 786s parsing sequence Sim.pm.1... 786s parsing sequence Sim.pm.2... 786s Parsed 86 reference bases 786s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '1' because it was < 2 characters long 786s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '4' because it was < 2 characters long 786s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '5' because it was < 2 characters long 786s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '6' because it was < 2 characters long 786s 17 reads; of these: 786s 17 (100.00%) were paired; of these: 786s 17 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 17 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 17 pairs aligned 0 times concordantly or discordantly; of these: 786s 34 mates make up the pairs; of these: 786s 34 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 0.00% overall alignment rate 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s --- Summary --- 786s Read 1 reference strings 786s Checked 0 alignments, 0 edits 786s --------------- 786s PASSED 786s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 786s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 786s *** Run 46 of 100 786s /usr/bin/bowtie2 --local --cp-ival 3 --nofw --trim3 4 --score-min L,4.39892759728657,9.72844644725227 --rdg 28.6289951132911,16.0267855312101 --cp-min 2 --np 4 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 786s /usr/bin/bowtie2 --local --cp-ival 3 --nofw --trim3 4 --score-min L,4.39892759728657,9.72844644725227 --rdg 28.6289951132911,16.0267855312101 --cp-min 2 --np 4 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 786s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '1' because it was < 2 characters long 786s Warning: skipping mate #2 of read '4' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #2 of read '4' because it was < 2 characters long 786s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '5' because it was < 2 characters long 786s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 786s Warning: skipping mate #1 of read '6' because it was < 2 characters long 786s 17 reads; of these: 786s 17 (100.00%) were paired; of these: 786s 17 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 17 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 17 pairs aligned 0 times concordantly or discordantly; of these: 786s 34 mates make up the pairs; of these: 786s 34 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 0.00% overall alignment rate 786s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 786s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 786s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 786s Flattened IUPAC characters 786s Mutating sequence Sim.pm.1 786s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutating sequence Sim.pm.2 786s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutated reference genome to subject genome 786s SNPs introduced: 4 786s Reference gaps introduced: 0 786s Read gaps introduced: 1 786s Rearrangements introduced: 0 786s Created read sampler 786s Sampling 4 reads 786s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 786s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 786s parsing sequence Sim.pm.1... 786s parsing sequence Sim.pm.2... 786s Parsed 86 reference bases 786s *** Run 47 of 100 786s /usr/bin/bowtie2 --cp-min 2 --cp-ival 3 --local -a -i S,1.48373903944987 --score-min L,8.79807417692445,4.25987044353457 --rfg 29.9311688882994 --norc -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 786s 4 reads; of these: 786s 4 (100.00%) were paired; of these: 786s 4 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 4 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 4 pairs aligned 0 times concordantly or discordantly; of these: 786s 8 mates make up the pairs; of these: 786s 8 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 0.00% overall alignment rate 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s Processing line... 786s --- Summary --- 786s Read 1 reference strings 786s /usr/bin/bowtie2 --cp-min 2 --cp-ival 3 --local -a -i S,1.48373903944987 --score-min L,8.79807417692445,4.25987044353457 --rfg 29.9311688882994 --norc -r -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 786s Checked 0 alignments, 0 edits 786s --------------- 786s PASSED 786s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 786s 4 reads; of these: 786s 4 (100.00%) were paired; of these: 786s 4 (100.00%) aligned concordantly 0 times 786s 0 (0.00%) aligned concordantly exactly 1 time 786s 0 (0.00%) aligned concordantly >1 times 786s ---- 786s 4 pairs aligned concordantly 0 times; of these: 786s 0 (0.00%) aligned discordantly 1 time 786s ---- 786s 4 pairs aligned 0 times concordantly or discordantly; of these: 786s 8 mates make up the pairs; of these: 786s 8 (100.00%) aligned 0 times 786s 0 (0.00%) aligned exactly 1 time 786s 0 (0.00%) aligned >1 times 786s 0.00% overall alignment rate 786s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 786s Flattened IUPAC characters 786s Mutating sequence Sim.pm.2 786s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutating sequence Sim.pm.1 786s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 786s Finished SNPs 786s Finished ref gaps 786s Finished read gaps 786s Mutated reference genome to subject genome 786s SNPs introduced: 8 786s Reference gaps introduced: 1 786s Read gaps introduced: 0 786s Rearrangements introduced: 0 786s Created read sampler 786s Sampling 87 reads 786s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 786s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 786s parsing sequence Sim.pm.1... 786s parsing sequence Sim.pm.2... 786s Parsed 86 reference bases 786s *** Run 48 of 100 786s /usr/bin/bowtie2 --trim5 6 --cp-min 9 -R 2 --score-min L,6.00155284867249,4.76120173963818 --rfg 5.53336871384473 --mm --n-ceil 1.33731696413455,1.30118818213278 --cp-ival 4 --nofw --mp 3.34103743498595,2.68614987624937 --trim3 9 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 787s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '3' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 787s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '6' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 787s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '10' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 787s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '13' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 787s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '14' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 787s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '17' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 787s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '28' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 787s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '29' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 787s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '30' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 787s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '38' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 787s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '39' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 787s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '41' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 787s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '43' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 787s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '45' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 787s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '50' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 787s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '51' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 787s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '52' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 787s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '53' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 787s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '62' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 787s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '65' because it was < 2 characters long 787s Read 50 alignments... 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 787s Read 100 alignments... 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 787s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '68' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 787s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '69' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 787s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '79' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 787s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '80' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 787s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '81' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 787s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '82' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 787s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '84' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 787s 87 reads; of these: 787s 70 (80.46%) were paired; of these: 787s 70 (100.00%) aligned concordantly 0 times 787s 0 (0.00%) aligned concordantly exactly 1 time 787s 0 (0.00%) aligned concordantly >1 times 787s ---- 787s 70 pairs aligned concordantly 0 times; of these: 787s 0 (0.00%) aligned discordantly 1 time 787s ---- 787s 70 pairs aligned 0 times concordantly or discordantly; of these: 787s 140 mates make up the pairs; of these: 787s 129 (92.14%) aligned 0 times 787s 8 (5.71%) aligned exactly 1 time 787s 3 (2.14%) aligned >1 times 787s 17 (19.54%) were unpaired; of these: 787s 14 (82.35%) aligned 0 times 787s 3 (17.65%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 8.92% overall alignment rate 787s Read 150 alignments... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s /usr/bin/bowtie2 --trim5 6 --cp-min 9 -R 2 --score-min L,6.00155284867249,4.76120173963818 --rfg 5.53336871384473 --mm --n-ceil 1.33731696413455,1.30118818213278 --cp-ival 4 --nofw --mp 3.34103743498595,2.68614987624937 --trim3 9 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s ATTCGAATCATGAC 787s ATTCGAATCATGAC 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s AATCATGACTGGATCTC 787s AATCATGACTGGATCTC 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s ATCATGACTGGA 787s ATCATGACTGGA 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s ATTCGAA 787s ATTCGAA 787s Processing line... 787s Processing line... 787s GGGCCACCGG 787s GGGCCACCGG 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s CATGACT 787s CATGACT 787s Processing line... 787s Processing line... 787s Processing line... 787s ATCATGACTGG 787s ATCATGACTGG 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s TTC 787s TTC 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s ATCATGACTGGA 787s ATCATGACTGGA 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s CAATTCGAATCATGACTGGATCTC 787s CAATTCGAATCATGACTGGATCTC 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s AGG 787s AGG 787s Processing line... 787s Processing line... 787s TGACTGGAT 787s TGACTGGAT 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s CGAAT 787s CGAAT 787s Processing line... 787s CAC 787s CAC 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s --- Summary --- 787s Read 1 reference strings 787s Checked 14 alignments, 0 edits 787s --------------- 787s PASSED 787s ALSO checking that bowtie2 and bowtie2-align match up 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 787s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '3' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 787s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '6' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 787s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '10' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 787s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '13' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 787s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '14' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 787s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '17' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 787s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '28' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 787s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '29' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 787s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '30' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 787s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '38' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 787s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '39' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 787s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '41' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 787s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '43' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 787s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '45' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 787s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '50' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 787s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '51' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 787s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '52' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 787s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '53' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 787s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '62' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 787s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '65' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 787s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '68' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 787s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '69' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 787s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '79' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 787s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '80' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 787s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '81' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 787s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '82' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 787s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '84' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 787s 87 reads; of these: 787s 70 (80.46%) were paired; of these: 787s 70 (100.00%) aligned concordantly 0 times 787s 0 (0.00%) aligned concordantly exactly 1 time 787s 0 (0.00%) aligned concordantly >1 times 787s ---- 787s 70 pairs aligned concordantly 0 times; of these: 787s 0 (0.00%) aligned discordantly 1 time 787s ---- 787s 70 pairs aligned 0 times concordantly or discordantly; of these: 787s 140 mates make up the pairs; of these: 787s 129 (92.14%) aligned 0 times 787s 8 (5.71%) aligned exactly 1 time 787s 3 (2.14%) aligned >1 times 787s 17 (19.54%) were unpaired; of these: 787s 14 (82.35%) aligned 0 times 787s 3 (17.65%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 8.92% overall alignment rate 787s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 787s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 787s /usr/bin/bowtie2 --trim5 6 --cp-min 9 -R 2 --score-min L,6.00155284867249,4.76120173963818 --rfg 5.53336871384473 --mm --n-ceil 1.33731696413455,1.30118818213278 --cp-ival 4 --nofw --mp 3.34103743498595,2.68614987624937 --trim3 9 -q -p 2 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 787s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '3' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 787s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '6' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 787s Warning: skipping mate #2 of read '10' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '10' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 787s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '13' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 787s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '14' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 787s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '17' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 787s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '28' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 787s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '29' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 787s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '30' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 787s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '38' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 787s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '39' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 787s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '41' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 787s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '43' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 787s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '45' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 787s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '50' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 787s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '51' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 787s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read '52' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 787s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '53' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 787s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '62' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 787s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '65' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 787s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '68' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 787s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '69' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 787s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '79' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 787s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '80' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 787s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '81' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 787s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '82' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 787s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '84' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 787s 87 reads; of these: 787s 70 (80.46%) were paired; of these: 787s 70 (100.00%) aligned concordantly 0 times 787s 0 (0.00%) aligned concordantly exactly 1 time 787s 0 (0.00%) aligned concordantly >1 times 787s ---- 787s 70 pairs aligned concordantly 0 times; of these: 787s 0 (0.00%) aligned discordantly 1 time 787s ---- 787s 70 pairs aligned 0 times concordantly or discordantly; of these: 787s 140 mates make up the pairs; of these: 787s 129 (92.14%) aligned 0 times 787s 8 (5.71%) aligned exactly 1 time 787s 3 (2.14%) aligned >1 times 787s 17 (19.54%) were unpaired; of these: 787s 14 (82.35%) aligned 0 times 787s 3 (17.65%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 8.92% overall alignment rate 787s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 787s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 787s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 787s Flattened IUPAC characters 787s Mutating sequence Sim.pm.1 787s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutating sequence Sim.pm.2 787s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutated reference genome to subject genome 787s SNPs introduced: 14 787s Reference gaps introduced: 0 787s Read gaps introduced: 0 787s Rearrangements introduced: 0 787s Created read sampler 787s Sampling 115 reads 787s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 787s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 787s parsing sequence Sim.pm.1... 787s parsing sequence Sim.pm.2... 787s Parsed 86 reference bases 787s *** Run 49 of 100 787s /usr/bin/bowtie2 --cp-min 6 --local --cp-ival 2 --n-ceil 0.596340438439016,0.410990897069791 --nofw --trim3 1 --score-min L,7.3094641535098,1.83350515544784 --rfg 49.9576742860499,19.9484889202852 --trim5 2 --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq 787s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 787s 115 reads; of these: 787s 115 (100.00%) were unpaired; of these: 787s 115 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s Read 50 alignments... 787s Read 100 alignments... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s /usr/bin/bowtie2 --cp-min 6 --local --cp-ival 2 --n-ceil 0.596340438439016,0.410990897069791 --nofw --trim3 1 --score-min L,7.3094641535098,1.83350515544784 --rfg 49.9576742860499,19.9484889202852 --trim5 2 --qseq -p 2 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s --- Summary --- 787s Read 1 reference strings 787s Checked 0 alignments, 0 edits 787s --------------- 787s PASSED 787s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 787s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_109_109_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_109_109_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_111_111_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 787s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 787s 115 reads; of these: 787s 115 (100.00%) were unpaired; of these: 787s 115 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 787s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 787s Flattened IUPAC characters 787s Mutating sequence Sim.pm.1 787s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutating sequence Sim.pm.2 787s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutated reference genome to subject genome 787s SNPs introduced: 9 787s Reference gaps introduced: 1 787s Read gaps introduced: 0 787s Rearrangements introduced: 1 787s Created read sampler 787s Sampling 104 reads 787s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 787s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 787s parsing sequence Sim.pm.1... 787s parsing sequence Sim.pm.2... 787s Parsed 86 reference bases 787s *** Run 50 of 100 787s /usr/bin/bowtie2 -M 5 --score-min L,3.51966896661178,6.17431004057469 --norc --np 1 --trim3 0 --nofw --cp-min 3 --cp-ival 1 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 787s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 787s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '23' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 787s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '62' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 787s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '64' because it was < 2 characters long 787s Read 50 alignments... 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 787s Read 100 alignments... 787s 104 reads; of these: 787s 104 (100.00%) were paired; of these: 787s 104 (100.00%) aligned concordantly 0 times 787s 0 (0.00%) aligned concordantly exactly 1 time 787s 0 (0.00%) aligned concordantly >1 times 787s ---- 787s 104 pairs aligned concordantly 0 times; of these: 787s 0 (0.00%) aligned discordantly 1 time 787s ---- 787s 104 pairs aligned 0 times concordantly or discordantly; of these: 787s 208 mates make up the pairs; of these: 787s 208 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s Read 150 alignments... 787s Read 200 alignments... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s --- Summary --- 787s Read 1 reference strings 787s Checked 0 alignments, 0 edits 787s --------------- 787s PASSED 787s ALSO checking that bowtie2 and bowtie2-align match up 787s /usr/bin/bowtie2 -M 5 --score-min L,3.51966896661178,6.17431004057469 --norc --np 1 --trim3 0 --nofw --cp-min 3 --cp-ival 1 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 787s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 787s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '23' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 787s Warning: skipping mate #1 of read '62' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '62' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 787s Warning: skipping mate #1 of read '64' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read '64' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 787s 104 reads; of these: 787s 104 (100.00%) were paired; of these: 787s 104 (100.00%) aligned concordantly 0 times 787s 0 (0.00%) aligned concordantly exactly 1 time 787s 0 (0.00%) aligned concordantly >1 times 787s ---- 787s 104 pairs aligned concordantly 0 times; of these: 787s 0 (0.00%) aligned discordantly 1 time 787s ---- 787s 104 pairs aligned 0 times concordantly or discordantly; of these: 787s 208 mates make up the pairs; of these: 787s 208 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 787s Flattened IUPAC characters 787s Mutating sequence Sim.pm.1 787s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutating sequence Sim.pm.2 787s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutated reference genome to subject genome 787s SNPs introduced: 12 787s Reference gaps introduced: 1 787s Read gaps introduced: 1 787s Rearrangements introduced: 1 787s Created read sampler 787s Sampling 86 reads 787s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 787s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 787s parsing sequence Sim.pm.1... 787s parsing sequence Sim.pm.2... 787s Parsed 86 reference bases 787s *** Run 51 of 100 787s /usr/bin/bowtie2 --mp 7.8169993574009,4.07977134537909 -N 0 -L12 --cp-ival 1 --local --rfg 12.751762366807 --rdg 49.8978358266484,19.6945768604237 --score-min L,9.53696187848307,9.03830656374621 --mm --cp-min 5 -R 4 --norc -i S,2.96050952078929 --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq 787s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 787s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 787s 86 reads; of these: 787s 86 (100.00%) were unpaired; of these: 787s 86 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s Read 50 alignments... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s --- Summary --- 787s Read 1 reference strings 787s Checked 0 alignments, 0 edits 787s --------------- 787s PASSED 787s Flattened IUPAC characters 787s Mutating sequence Sim.pm.1 787s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutating sequence Sim.pm.2 787s Introducing 4 SNPs, 1/2 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutated reference genome to subject genome 787s SNPs introduced: 10 787s Reference gaps introduced: 2 787s Read gaps introduced: 2 787s Rearrangements introduced: 0 787s Created read sampler 787s Sampling 122 reads 787s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 787s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 787s *** Run 52 of 100 787s /usr/bin/bowtie2 --cp-min 5 --ma 2.5139491463479 --np 20 --norc -k 4 --trim5 3 --cp-ival 1 --mp 8.14772135371171,7.67356516525757 --nofw --trim3 5 --gbar 6 --rdg 19.5436870568494 --rfg 43.3741290815179,14.685384801709 --score-min L,7.91699517701966,7.50322556159188 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 787s parsing sequence Sim.pm.1... 787s parsing sequence Sim.pm.2... 787s Parsed 86 reference bases 787s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 787s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 787s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 787s Read 50 alignments... 787s Read 100 alignments... 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 787s 122 reads; of these: 787s 101 (82.79%) were paired; of these: 787s 101 (100.00%) aligned concordantly 0 times 787s 0 (0.00%) aligned concordantly exactly 1 time 787s 0 (0.00%) aligned concordantly >1 times 787s ---- 787s 101 pairs aligned concordantly 0 times; of these: 787s 0 (0.00%) aligned discordantly 1 time 787s ---- 787s 101 pairs aligned 0 times concordantly or discordantly; of these: 787s 202 mates make up the pairs; of these: 787s 202 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 21 (17.21%) were unpaired; of these: 787s 21 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s Read 150 alignments... 787s Read 200 alignments... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s /usr/bin/bowtie2 --cp-min 5 --ma 2.5139491463479 --np 20 --norc -k 4 --trim5 3 --cp-ival 1 --mp 8.14772135371171,7.67356516525757 --nofw --trim3 5 --gbar 6 --rdg 19.5436870568494 --rfg 43.3741290815179,14.685384801709 --score-min L,7.91699517701966,7.50322556159188 --qseq -p 4 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s --- Summary --- 787s Read 1 reference strings 787s Checked 0 alignments, 0 edits 787s --------------- 787s PASSED 787s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 787s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 787s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 787s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because length (1) <= # seed mismatches (0) 787s Warning: skipping mate #2 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_106_106_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 787s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 787s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 787s Warning: skipping mate #1 of read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 787s 122 reads; of these: 787s 101 (82.79%) were paired; of these: 787s 101 (100.00%) aligned concordantly 0 times 787s 0 (0.00%) aligned concordantly exactly 1 time 787s 0 (0.00%) aligned concordantly >1 times 787s ---- 787s 101 pairs aligned concordantly 0 times; of these: 787s 0 (0.00%) aligned discordantly 1 time 787s ---- 787s 101 pairs aligned 0 times concordantly or discordantly; of these: 787s 202 mates make up the pairs; of these: 787s 202 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 21 (17.21%) were unpaired; of these: 787s 21 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 787s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 787s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 787s Flattened IUPAC characters 787s Mutating sequence Sim.pm.2 787s Introducing 1 SNPs, 2/0 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutating sequence Sim.pm.1 787s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutated reference genome to subject genome 787s SNPs introduced: 5 787s Reference gaps introduced: 2 787s Read gaps introduced: 0 787s Rearrangements introduced: 1 787s Created read sampler 787s Sampling 66 reads 787s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 787s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 787s parsing sequence Sim.pm.1... 787s parsing sequence Sim.pm.2... 787s Parsed 86 reference bases 787s *** Run 53 of 100 787s /usr/bin/bowtie2 --cp-min 2 --np 1 --trim5 8 -D 27 --cp-ival 1 --local --mp 3.27382870916065,1.7112910134996 --trim3 7 --rdg 24.6281026026182 --rfg 7.42211026878998,15.2046581038255 --score-min L,5.75269390315701,3.90774934280603 --mm -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 787s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '2' because it was < 2 characters long 787s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '3' because it was < 2 characters long 787s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '4' because it was < 2 characters long 787s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '5' because it was < 2 characters long 787s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '6' because it was < 2 characters long 787s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '7' because it was < 2 characters long 787s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '8' because it was < 2 characters long 787s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '9' because it was < 2 characters long 787s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '10' because it was < 2 characters long 787s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '12' because it was < 2 characters long 787s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '13' because it was < 2 characters long 787s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '14' because it was < 2 characters long 787s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '15' because it was < 2 characters long 787s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '18' because it was < 2 characters long 787s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '21' because it was < 2 characters long 787s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '22' because it was < 2 characters long 787s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '23' because it was < 2 characters long 787s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '24' because it was < 2 characters long 787s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '29' because it was < 2 characters long 787s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '31' because it was < 2 characters long 787s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '33' because it was < 2 characters long 787s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '34' because it was < 2 characters long 787s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '40' because it was < 2 characters long 787s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '46' because it was < 2 characters long 787s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '48' because it was < 2 characters long 787s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '50' because it was < 2 characters long 787s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '58' because it was < 2 characters long 787s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '60' because it was < 2 characters long 787s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '63' because it was < 2 characters long 787s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '65' because it was < 2 characters long 787s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '66' because it was < 2 characters long 787s 66 reads; of these: 787s 66 (100.00%) were unpaired; of these: 787s 66 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s Read 50 alignments... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s --- Summary --- 787s Read 1 reference strings 787s Checked 0 alignments, 0 edits 787s --------------- 787s PASSED 787s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 787s /usr/bin/bowtie2 --cp-min 2 --np 1 --trim5 8 -D 27 --cp-ival 1 --local --mp 3.27382870916065,1.7112910134996 --trim3 7 --rdg 24.6281026026182 --rfg 7.42211026878998,15.2046581038255 --score-min L,5.75269390315701,3.90774934280603 --mm -f -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 787s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '2' because it was < 2 characters long 787s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '3' because it was < 2 characters long 787s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '4' because it was < 2 characters long 787s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '5' because it was < 2 characters long 787s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '6' because it was < 2 characters long 787s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '7' because it was < 2 characters long 787s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '8' because it was < 2 characters long 787s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '9' because it was < 2 characters long 787s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '10' because it was < 2 characters long 787s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '12' because it was < 2 characters long 787s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '13' because it was < 2 characters long 787s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '14' because it was < 2 characters long 787s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '15' because it was < 2 characters long 787s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '18' because it was < 2 characters long 787s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '21' because it was < 2 characters long 787s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '22' because it was < 2 characters long 787s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '23' because it was < 2 characters long 787s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '24' because it was < 2 characters long 787s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '29' because it was < 2 characters long 787s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '31' because it was < 2 characters long 787s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '33' because it was < 2 characters long 787s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '34' because it was < 2 characters long 787s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '40' because it was < 2 characters long 787s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '46' because it was < 2 characters long 787s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '48' because it was < 2 characters long 787s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '50' because it was < 2 characters long 787s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '58' because it was < 2 characters long 787s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '60' because it was < 2 characters long 787s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '63' because it was < 2 characters long 787s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '65' because it was < 2 characters long 787s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 787s Warning: skipping read '66' because it was < 2 characters long 787s 66 reads; of these: 787s 66 (100.00%) were unpaired; of these: 787s 66 (100.00%) aligned 0 times 787s 0 (0.00%) aligned exactly 1 time 787s 0 (0.00%) aligned >1 times 787s 0.00% overall alignment rate 787s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 787s *** Run 54 of 100 787s /usr/bin/bowtie2 --score-min L,2.60644978403497,2.89658252997767 --norc --mp 8.5462980356232,5.17322156984538 --cp-min 5 -D 7 --cp-ival 1 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 787s Flattened IUPAC characters 787s Mutating sequence Sim.pm.2 787s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutating sequence Sim.pm.1 787s Introducing 7 SNPs, 0/1 ref/read gaps, and 3 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutated reference genome to subject genome 787s SNPs introduced: 9 787s Reference gaps introduced: 0 787s Read gaps introduced: 1 787s Rearrangements introduced: 3 787s Created read sampler 787s Sampling 157 reads 787s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 787s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 787s parsing sequence Sim.pm.1... 787s parsing sequence Sim.pm.2... 787s Parsed 86 reference bases 787s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 787s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '33' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 787s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '39' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 787s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '62' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 787s Warning: skipping read '120' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '120' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 787s Warning: skipping read '122' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '122' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 787s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '124' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 787s Warning: skipping read '129' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '129' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 787s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '130' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 787s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '139' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 787s 157 reads; of these: 787s 157 (100.00%) were unpaired; of these: 787s 140 (89.17%) aligned 0 times 787s 8 (5.10%) aligned exactly 1 time 787s 9 (5.73%) aligned >1 times 787s 10.83% overall alignment rate 787s Read 50 alignments... 787s Read 100 alignments... 787s Read 150 alignments... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s TTC 787s TTC 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s GT 787s GT 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s GAC 787s GAC 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s AA 787s AA 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s AG 787s AG 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s AG 787s AG 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s GA 787s GA 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s GGG 787s GGG 787s Processing line... 787s Processing line... 787s CC 787s CC 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s GGATCT 787s GGATCT 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s GAT 787s GAT 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s AAGGG 787s AAGGG 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s ATCATGACTGG 787s ATCATGACTGG 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s TC 787s TC 787s Processing line... 787s Processing line... 787s Processing line... 787s GTGCAATTCGAATCATGACTGGATCT 787s GTGCAATTCGAATCATGACTGGATCT 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s GAAT 787s GAAT 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s Processing line... 787s GG 787s GG 787s --- Summary --- 787s Read 1 reference strings 787s Checked 17 alignments, 0 edits 787s --------------- 787s PASSED 787s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 787s /usr/bin/bowtie2 --score-min L,2.60644978403497,2.89658252997767 --norc --mp 8.5462980356232,5.17322156984538 --cp-min 5 -D 7 --cp-ival 1 -r -p 2 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 787s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 787s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '33' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 787s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '39' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 787s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '62' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 787s Warning: skipping read '120' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '120' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 787s Warning: skipping read '122' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '122' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 787s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '124' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 787s Warning: skipping read '129' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '129' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 787s Warning: skipping read '130' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '130' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 787s Warning: skipping read '139' because length (1) <= # seed mismatches (0) 787s Warning: skipping read '139' because it was < 2 characters long 787s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 787s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 787s 157 reads; of these: 787s 157 (100.00%) were unpaired; of these: 787s 140 (89.17%) aligned 0 times 787s 8 (5.10%) aligned exactly 1 time 787s 9 (5.73%) aligned >1 times 787s 10.83% overall alignment rate 787s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 787s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 787s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 787s Flattened IUPAC characters 787s Mutating sequence Sim.pm.2 787s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutating sequence Sim.pm.1 787s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 787s Finished SNPs 787s Finished ref gaps 787s Finished read gaps 787s Mutated reference genome to subject genome 787s SNPs introduced: 2 787s Reference gaps introduced: 0 787s Read gaps introduced: 1 787s Rearrangements introduced: 0 787s Created read sampler 787s Sampling 166 reads 787s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 787s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 787s parsing sequence Sim.pm.1... 787s parsing sequence Sim.pm.2... 787s Parsed 86 reference bases 787s *** Run 55 of 100 787s /usr/bin/bowtie2 --cp-min 5 --score-min L,2.71512379068207,4.40558778237317 --cp-ival 3 --local --mp 7.12987896662192,3.57718306968946 -N 1 -L25 --trim3 5 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 788s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '1' because it was < 2 characters long 788s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '6' because it was < 2 characters long 788s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '12' because it was < 2 characters long 788s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '13' because it was < 2 characters long 788s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '15' because it was < 2 characters long 788s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '43' because it was < 2 characters long 788s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '55' because it was < 2 characters long 788s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '58' because it was < 2 characters long 788s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '62' because it was < 2 characters long 788s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 788s Warning: skipping read '65' because it was < 2 characters long 788s Read 50 alignments... 788s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '68' because it was < 2 characters long 788s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '74' because it was < 2 characters long 788s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '76' because it was < 2 characters long 788s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '77' because it was < 2 characters long 788s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (1) 788s Warning: skipping mate #2 of read '91' because it was < 2 characters long 788s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 788s Warning: skipping read '99' because it was < 2 characters long 788s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '104' because it was < 2 characters long 788s Warning: skipping mate #1 of read '141' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '141' because it was < 2 characters long 788s Warning: skipping mate #2 of read '142' because length (1) <= # seed mismatches (1) 788s Warning: skipping mate #2 of read '142' because it was < 2 characters long 788s Read 100 alignments... 788s Warning: skipping read '156' because length (0) <= # seed mismatches (1) 788s Warning: skipping read '156' because it was < 2 characters long 788s Read 150 alignments... 788s Read 200 alignments... 788s 166 reads; of these: 788s 141 (84.94%) were paired; of these: 788s 141 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 141 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 141 pairs aligned 0 times concordantly or discordantly; of these: 788s 282 mates make up the pairs; of these: 788s 282 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 25 (15.06%) were unpaired; of these: 788s 25 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 0.00% overall alignment rate 788s Read 250 alignments... 788s Read 300 alignments... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s /usr/bin/bowtie2 --cp-min 5 --score-min L,2.71512379068207,4.40558778237317 --cp-ival 3 --local --mp 7.12987896662192,3.57718306968946 -N 1 -L25 --trim3 5 -q -p 4 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s 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Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s --- Summary --- 788s Read 1 reference strings 788s Checked 0 alignments, 0 edits 788s --------------- 788s PASSED 788s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 788s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '1' because it was < 2 characters long 788s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '6' because it was < 2 characters long 788s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '12' because it was < 2 characters long 788s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '13' because it was < 2 characters long 788s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '15' because it was < 2 characters long 788s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '43' because it was < 2 characters long 788s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '55' because it was < 2 characters long 788s Warning: skipping mate #1 of read '58' because length (1) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '58' because it was < 2 characters long 788s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '62' because it was < 2 characters long 788s Warning: skipping read '65' because length (0) <= # seed mismatches (1) 788s Warning: skipping read '65' because it was < 2 characters long 788s Warning: skipping mate #1 of read '68' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '68' because it was < 2 characters long 788s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '74' because it was < 2 characters long 788s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '76' because it was < 2 characters long 788s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '77' because it was < 2 characters long 788s Warning: skipping mate #2 of read '91' because length (1) <= # seed mismatches (1) 788s Warning: skipping mate #2 of read '91' because it was < 2 characters long 788s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 788s Warning: skipping read '99' because it was < 2 characters long 788s Warning: skipping mate #1 of read '104' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '104' because it was < 2 characters long 788s Warning: skipping mate #1 of read '141' because length (0) <= # seed mismatches (1) 788s Warning: skipping mate #1 of read '141' because it was < 2 characters long 788s Warning: skipping mate #2 of read '142' because length (1) <= # seed mismatches (1) 788s Warning: skipping mate #2 of read '142' because it was < 2 characters long 788s Warning: skipping read '156' because length (0) <= # seed mismatches (1) 788s Warning: skipping read '156' because it was < 2 characters long 788s 166 reads; of these: 788s 141 (84.94%) were paired; of these: 788s 141 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 141 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 141 pairs aligned 0 times concordantly or discordantly; of these: 788s 282 mates make up the pairs; of these: 788s 282 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 25 (15.06%) were unpaired; of these: 788s 25 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 0.00% overall alignment rate 788s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 788s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 788s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 788s Flattened IUPAC characters 788s Mutating sequence Sim.pm.1 788s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutating sequence Sim.pm.2 788s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutated reference genome to subject genome 788s SNPs introduced: 5 788s Reference gaps introduced: 0 788s Read gaps introduced: 0 788s Rearrangements introduced: 1 788s Created read sampler 788s Sampling 110 reads 788s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 788s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 788s parsing sequence Sim.pm.1... 788s parsing sequence Sim.pm.2... 788s *** Run 56 of 100 788s /usr/bin/bowtie2 --mp 4.76109130805953,3.3475582625449 --cp-ival 1 --cp-min 3 -R 3 --trim3 9 --rfg 11.2817107056945 --score-min L,8.68303977235145,9.21686733534268 --gbar 2 --np 22 --mm --trim5 8 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 788s Parsed 86 reference bases 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 788s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '2' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 788s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '9' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 788s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '10' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 788s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '13' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 788s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '14' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 788s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '15' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 788s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '19' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 788s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '20' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 788s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '26' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 788s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '36' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 788s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '39' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 788s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '45' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 788s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '46' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 788s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '53' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 788s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '55' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 788s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '57' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 788s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '60' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 788s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '65' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 788s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '67' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 788s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '68' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 788s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '70' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 788s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '77' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 788s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '81' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 788s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '82' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 788s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '83' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 788s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '87' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 788s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '88' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 788s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '99' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 788s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '101' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 788s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '105' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 788s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '107' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 788s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '109' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 788s Read 50 alignments... 788s 110 reads; of these: 788s 80 (72.73%) were paired; of these: 788s 80 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 80 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 80 pairs aligned 0 times concordantly or discordantly; of these: 788s 160 mates make up the pairs; of these: 788s 143 (89.38%) aligned 0 times 788s 10 (6.25%) aligned exactly 1 time 788s 7 (4.38%) aligned >1 times 788s 30 (27.27%) were unpaired; of these: 788s 26 (86.67%) aligned 0 times 788s 4 (13.33%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 11.05% overall alignment rate 788s Read 100 alignments... 788s Read 150 alignments... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s ATC 788s ATC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CC 788s CC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGGC 788s GGGC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GCAATTCGAATCATGACTGGATCT 788s GCAATTCGAATCATGACTGGATCT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s TTCG 788s TTCG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GAATCATGACTGGATC 788s GAATCATGACTGGATC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s ATCATGACTGGATCTCA 788s ATCATGACTGGATCTCA 788s Processing line... 788s Processing line... 788s TCATG 788s TCATG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s TCT 788s TCT 788s Processing line... 788s Processing line... 788s Processing line... 788s GCAATTCGAATCA 788s GCAATTCGAATCA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s AT 788s AT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s ACC 788s ACC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGCCACCGG 788s GGCCACCGG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GCAATTCGAATCATGACTGGA 788s GCAATTCGAATCATGACTGGA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s TCATGACT 788s TCATGACT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGGCCACC 788s GGGCCACC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CTGGATCTCA 788s CTGGATCTCA 788s Processing line... 788s Processing line... 788s AATTCGAATCATGA 788s AATTCGAATCATGA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GTGCAATTCGAATCATGACTGGATC 788s GTGCAATTCGAATCATGACTGGATC 788s Processing line... 788s Processing line... 788s Processing line... 788s TGTGCAATTCGAATCATGACTGGA 788s TGTGCAATTCGAATCATGACTGGA 788s Processing line... 788s Processing line... 788s Processing line... 788s GCAATTCGAA 788s GCAATTCGAA 788s Processing line... 788s --- Summary --- 788s Read 1 reference strings 788s Checked 21 alignments, 0 edits 788s --------------- 788s PASSED 788s ALSO checking that bowtie2 and bowtie2-align match up 788s /usr/bin/bowtie2 --mp 4.76109130805953,3.3475582625449 --cp-ival 1 --cp-min 3 -R 3 --trim3 9 --rfg 11.2817107056945 --score-min L,8.68303977235145,9.21686733534268 --gbar 2 --np 22 --mm --trim5 8 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 788s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '2' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 788s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '9' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 788s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '10' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 788s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '13' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 788s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '14' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 788s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '15' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 788s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '19' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 788s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '20' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 788s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '26' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 788s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '36' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 788s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '39' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 788s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '45' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 788s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '46' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 788s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '53' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 788s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '55' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 788s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '57' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 788s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '60' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 788s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '65' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 788s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '67' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 788s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '68' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 788s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '70' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 788s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '77' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 788s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '81' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 788s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '82' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 788s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '83' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 788s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '87' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 788s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '88' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 788s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '99' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 788s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '101' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 788s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '105' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 788s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '107' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 788s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '109' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 788s 110 reads; of these: 788s 80 (72.73%) were paired; of these: 788s 80 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 80 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 80 pairs aligned 0 times concordantly or discordantly; of these: 788s 160 mates make up the pairs; of these: 788s 143 (89.38%) aligned 0 times 788s 10 (6.25%) aligned exactly 1 time 788s 7 (4.38%) aligned >1 times 788s 30 (27.27%) were unpaired; of these: 788s 26 (86.67%) aligned 0 times 788s 4 (13.33%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 11.05% overall alignment rate 788s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 788s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 788s /usr/bin/bowtie2 --mp 4.76109130805953,3.3475582625449 --cp-ival 1 --cp-min 3 -R 3 --trim3 9 --rfg 11.2817107056945 --score-min L,8.68303977235145,9.21686733534268 --gbar 2 --np 22 --mm --trim5 8 -f -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 788s Warning: skipping mate #1 of read '2' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '2' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 788s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '9' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 788s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '10' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 788s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '13' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 788s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '14' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 788s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '15' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 788s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '19' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 788s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '20' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 788s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '26' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 788s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '36' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 788s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '39' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 788s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '45' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 788s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '46' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 788s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '53' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 788s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '55' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 788s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '57' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 788s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '60' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 788s Warning: skipping mate #1 of read '65' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '65' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 788s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '67' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 788s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '68' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 788s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '70' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 788s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 788s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '77' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 788s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '81' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 788s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '82' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 788s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '83' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 788s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '87' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 788s Warning: skipping mate #2 of read '88' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '88' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 788s Warning: skipping mate #1 of read '99' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '99' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 788s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '101' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 788s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '105' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 788s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '107' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 788s Warning: skipping mate #1 of read '109' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '109' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 788s 110 reads; of these: 788s 80 (72.73%) were paired; of these: 788s 80 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 80 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 80 pairs aligned 0 times concordantly or discordantly; of these: 788s 160 mates make up the pairs; of these: 788s 143 (89.38%) aligned 0 times 788s 10 (6.25%) aligned exactly 1 time 788s 7 (4.38%) aligned >1 times 788s 30 (27.27%) were unpaired; of these: 788s 26 (86.67%) aligned 0 times 788s 4 (13.33%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 11.05% overall alignment rate 788s Flattened IUPAC characters 788s Mutating sequence Sim.pm.2 788s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s *** Run 57 of 100 788s /usr/bin/bowtie2 --trim3 2 --cp-min 3 --cp-ival 2 --ma 28.5699818029294 --mp 7.85586565721248,2.63003501461492 --mm -a --np 1 --score-min L,8.40424405800213,4.81537909913213 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 788s Mutating sequence Sim.pm.1 788s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutated reference genome to subject genome 788s SNPs introduced: 7 788s Reference gaps introduced: 0 788s Read gaps introduced: 0 788s Rearrangements introduced: 0 788s Created read sampler 788s Sampling 145 reads 788s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 788s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 788s parsing sequence Sim.pm.1... 788s parsing sequence Sim.pm.2... 788s Parsed 86 reference bases 788s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 788s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '13' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 788s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '18' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 788s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '38' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 788s Read 50 alignments... 788s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 788s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '57' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 788s Read 100 alignments... 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 788s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '61' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 788s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '96' because it was < 2 characters long 788s Read 150 alignments... 788s Read 200 alignments... 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 788s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '101' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 788s Warning: skipping mate #2 of read '127' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '127' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 788s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '136' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 788s Read 250 alignments... 788s Read 300 alignments... 788s Read 350 alignments... 788s 145 reads; of these: 788s 138 (95.17%) were paired; of these: 788s 138 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 138 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 138 pairs aligned 0 times concordantly or discordantly; of these: 788s 276 mates make up the pairs; of these: 788s 242 (87.68%) aligned 0 times 788s 13 (4.71%) aligned exactly 1 time 788s 21 (7.61%) aligned >1 times 788s 7 (4.83%) were unpaired; of these: 788s 7 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 12.01% overall alignment rate 788s Read 400 alignments... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CGGGAGGC 788s CGGGAGGC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CCT 788s CCT 788s Processing line... 788s AGG 788s AGG 788s Processing line... 788s AGG 788s AGG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CCGGGA 788s CCGGGA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s AAT 788s AAT 788s Processing line... 788s AAT 788s AAT 788s Processing line... 788s AAT 788s AAT 788s Processing line... 788s AAT 788s AAT 788s Processing line... 788s ATT 788s ATT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CT 788s CT 788s Processing line... 788s CT 788s CT 788s Processing line... 788s AG 788s AG 788s Processing line... 788s CT 788s CT 788s Processing line... 788s AG 788s AG 788s Processing line... 788s CT 788s CT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s AA 788s AA 788s Processing line... 788s AA 788s AA 788s Processing line... 788s AA 788s AA 788s Processing line... 788s TT 788s TT 788s Processing line... 788s AA 788s AA 788s Processing line... 788s AA 788s AA 788s Processing line... 788s TT 788s TT 788s Processing line... 788s AA 788s AA 788s Processing line... 788s AA 788s AA 788s Processing line... 788s AA 788s AA 788s Processing line... 788s TT 788s TT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s AGGG 788s AGGG 788s Processing line... 788s CCCT 788s CCCT 788s Processing line... 788s GGATC 788s GGATC 788s Processing line... 788s GGCC 788s GGCC 788s Processing line... 788s GGCC 788s GGCC 788s Processing line... 788s GGCC 788s GGCC 788s Processing line... 788s GGCC 788s GGCC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGCCACCGGGAGGC 788s GGCCACCGGGAGGC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s Processing line... 788s GCC 788s GCC 788s Processing line... 788s GCC 788s GCC 788s Processing line... 788s GCC 788s GCC 788s Processing line... 788s GGC 788s GGC 788s Processing line... 788s GGC 788s GGC 788s Processing line... 788s GGC 788s GGC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CCA 788s CCA 788s Processing line... 788s CCA 788s CCA 788s Processing line... 788s CCA 788s CCA 788s Processing line... 788s TGG 788s TGG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CCA 788s CCA 788s Processing line... 788s CCA 788s CCA 788s Processing line... 788s CCA 788s CCA 788s Processing line... 788s TGG 788s TGG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGCCACCGGGA 788s GGCCACCGGGA 788s Processing line... 788s Processing line... 788s TTC 788s TTC 788s Processing line... 788s TTC 788s TTC 788s Processing line... 788s GAA 788s GAA 788s Processing line... 788s Processing line... 788s TCTT 788s TCTT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GCC 788s GCC 788s Processing line... 788s GCC 788s GCC 788s Processing line... 788s GCC 788s GCC 788s Processing line... 788s GGC 788s GGC 788s Processing line... 788s GGC 788s GGC 788s Processing line... 788s GGC 788s GGC 788s Processing line... 788s Processing line... 788s GCA 788s GCA 788s Processing line... 788s TGC 788s TGC 788s Processing line... 788s GCA 788s GCA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s TGT 788s TGT 788s Processing line... 788s Processing line... 788s CGGGAGG 788s CGGGAGG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GCCAC 788s GCCAC 788s Processing line... 788s GCCAC 788s GCCAC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGGCCACCGGGAGGC 788s GGGCCACCGGGAGGC 788s Processing line... 788s Processing line... 788s ACCGGGAGG 788s ACCGGGAGG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CAA 788s CAA 788s Processing line... 788s CAA 788s CAA 788s Processing line... 788s CAA 788s CAA 788s Processing line... 788s CAA 788s CAA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CCGCCACCCTCTTTCCC 788s CCGCCACCCTCTTTCCC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s Processing line... 788s TGTGCAATTC 788s TGTGCAATTC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s GG 788s GG 788s Processing line... 788s GG 788s GG 788s Processing line... 788s CC 788s CC 788s Processing line... 788s CC 788s CC 788s Processing line... 788s Processing line... 788s CCCT 788s CCCT 788s Processing line... 788s AGGG 788s AGGG 788s Processing line... 788s Processing line... 788s CACCGGGA 788s CACCGGGA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GCCA 788s GCCA 788s Processing line... 788s GCCA 788s GCCA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s --- Summary --- 788s Read 1 reference strings 788s Checked 156 alignments, 0 edits 788s --------------- 788s PASSED 788s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 788s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 788s /usr/bin/bowtie2 --trim3 2 --cp-min 3 --cp-ival 2 --ma 28.5699818029294 --mp 7.85586565721248,2.63003501461492 --mm -a --np 1 --score-min L,8.40424405800213,4.81537909913213 -r -p 4 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 788s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '13' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 788s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '18' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 788s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '38' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 788s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '57' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 788s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '61' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 788s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '96' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 788s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '101' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 788s Warning: skipping mate #2 of read '127' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '127' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 788s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '136' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 788s 145 reads; of these: 788s 138 (95.17%) were paired; of these: 788s 138 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 138 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 138 pairs aligned 0 times concordantly or discordantly; of these: 788s 276 mates make up the pairs; of these: 788s 242 (87.68%) aligned 0 times 788s 13 (4.71%) aligned exactly 1 time 788s 21 (7.61%) aligned >1 times 788s 7 (4.83%) were unpaired; of these: 788s 7 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 12.01% overall alignment rate 788s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 788s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 788s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 788s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 788s /usr/bin/bowtie2 --trim3 2 --cp-min 3 --cp-ival 2 --ma 28.5699818029294 --mp 7.85586565721248,2.63003501461492 --mm -a --np 1 --score-min L,8.40424405800213,4.81537909913213 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 788s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 788s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '13' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 788s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '18' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 788s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '38' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 788s Warning: skipping mate #2 of read '57' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '57' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 788s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '61' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 788s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '96' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 788s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '101' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 788s Warning: skipping mate #2 of read '127' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '127' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 788s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 788s Warning: skipping mate #1 of read '136' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '136' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 788s 145 reads; of these: 788s 138 (95.17%) were paired; of these: 788s 138 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 138 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 138 pairs aligned 0 times concordantly or discordantly; of these: 788s 276 mates make up the pairs; of these: 788s 242 (87.68%) aligned 0 times 788s 13 (4.71%) aligned exactly 1 time 788s 21 (7.61%) aligned >1 times 788s 7 (4.83%) were unpaired; of these: 788s 7 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 12.01% overall alignment rate 788s Flattened IUPAC characters 788s Mutating sequence Sim.pm.2 788s *** Run 58 of 100 788s /usr/bin/bowtie2 --trim5 7 -a --rdg 38.4197080054671 --score-min L,4.67446635120066,2.29286212515704 --np 4 --ma 30.5039358152238 --cp-ival 1 --cp-min 9 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 788s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutating sequence Sim.pm.1 788s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutated reference genome to subject genome 788s SNPs introduced: 0 788s Reference gaps introduced: 1 788s Read gaps introduced: 0 788s Rearrangements introduced: 0 788s Created read sampler 788s Sampling 74 reads 788s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 788s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 788s parsing sequence Sim.pm.1... 788s parsing sequence Sim.pm.2... 788s Parsed 86 reference bases 788s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 788s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 788s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '14' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 788s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '17' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 788s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '18' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 788s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '20' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 788s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '22' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 788s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '31' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 788s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '36' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 788s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '37' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 788s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '44' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 788s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '62' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 788s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '64' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 788s Read 50 alignments... 788s Read 100 alignments... 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 788s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '72' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 788s 74 reads; of these: 788s 61 (82.43%) were paired; of these: 788s 61 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 61 pairs aligned concordantly 0 times; of these: 788s 2 (3.28%) aligned discordantly 1 time 788s ---- 788s 59 pairs aligned 0 times concordantly or discordantly; of these: 788s 118 mates make up the pairs; of these: 788s 98 (83.05%) aligned 0 times 788s 15 (12.71%) aligned exactly 1 time 788s 5 (4.24%) aligned >1 times 788s 13 (17.57%) were unpaired; of these: 788s 10 (76.92%) aligned 0 times 788s 2 (15.38%) aligned exactly 1 time 788s 1 (7.69%) aligned >1 times 788s 20.00% overall alignment rate 788s Read 150 alignments... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s AGG 788s AGG 788s Processing line... 788s AGG 788s AGG 788s Processing line... 788s CCT 788s CCT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGGAGGCA 788s GGGAGGCA 788s Processing line... 788s Processing line... 788s TTCGAATCATG 788s TTCGAATCATG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s AT 788s AT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGATC 788s GGATC 788s Processing line... 788s Processing line... 788s Processing line... 788s ATGACTG 788s ATGACTG 788s Processing line... 788s Processing line... 788s TTCGAATCATGACTGGAT 788s TTCGAATCATGACTGGAT 788s Processing line... 788s Processing line... 788s Processing line... 788s ATGACTGG 788s ATGACTGG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GGGAGGCAC 788s GGGAGGCAC 788s Processing line... 788s GCAAT 788s GCAAT 788s Processing line... 788s AAGGGCCACCGGGAGGCA 788s AAGGGCCACCGGGAGGCA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s TCATGACTGGA 788s TCATGACTGGA 788s Processing line... 788s Processing line... 788s AAGGGCCACCGGGAGG 788s AAGGGCCACCGGGAGG 788s Processing line... 788s Processing line... 788s TGA 788s TGA 788s Processing line... 788s TCA 788s TCA 788s Processing line... 788s TCA 788s TCA 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GAATCATGACTGGATCTCAAAT 788s GAATCATGACTGGATCTCAAAT 788s Processing line... 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s Processing line... 788s CG 788s CG 788s /usr/bin/bowtie2 --trim5 7 -a --rdg 38.4197080054671 --score-min L,4.67446635120066,2.29286212515704 --np 4 --ma 30.5039358152238 --cp-ival 1 --cp-min 9 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 788s Processing line... 788s CG 788s CG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s ACT 788s ACT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s GCAATT 788s GCAATT 788s Processing line... 788s Processing line... 788s TCGAATCATGACTGGATC 788s TCGAATCATGACTGGATC 788s Processing line... 788s CACCGGGAGGCAC 788s CACCGGGAGGCAC 788s Processing line... 788s TTCGAATCATGACTGGATCTC 788s TTCGAATCATGACTGGATCTC 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s AAAT 788s AAAT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s TGTGCAA 788s TGTGCAA 788s Processing line... 788s Processing line... 788s AGG 788s AGG 788s Processing line... 788s AGG 788s AGG 788s Processing line... 788s CCT 788s CCT 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s TCGAATCATG 788s TCGAATCATG 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s CTG 788s CTG 788s Processing line... 788s Processing line... 788s GTGC 788s GTGC 788s Processing line... 788s GCAC 788s GCAC 788s Processing line... 788s --- Summary --- 788s Read 1 reference strings 788s Checked 56 alignments, 0 edits 788s --------------- 788s PASSED 788s ALSO checking that bowtie2 and bowtie2-align match up 788s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 788s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 788s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '14' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 788s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '17' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 788s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '18' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 788s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '20' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 788s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '22' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 788s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '31' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 788s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '36' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 788s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '37' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 788s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 788s Warning: skipping read '44' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 788s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '62' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 788s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '64' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 788s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '72' because it was < 2 characters long 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 788s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 788s 74 reads; of these: 788s 61 (82.43%) were paired; of these: 788s 61 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 61 pairs aligned concordantly 0 times; of these: 788s 2 (3.28%) aligned discordantly 1 time 788s ---- 788s 59 pairs aligned 0 times concordantly or discordantly; of these: 788s 118 mates make up the pairs; of these: 788s 98 (83.05%) aligned 0 times 788s 15 (12.71%) aligned exactly 1 time 788s 5 (4.24%) aligned >1 times 788s 13 (17.57%) were unpaired; of these: 788s 10 (76.92%) aligned 0 times 788s 2 (15.38%) aligned exactly 1 time 788s 1 (7.69%) aligned >1 times 788s 20.00% overall alignment rate 788s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 788s Flattened IUPAC characters 788s Mutating sequence Sim.pm.2 788s Introducing 10 SNPs, 1/0 ref/read gaps, and 0 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutating sequence Sim.pm.1 788s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutated reference genome to subject genome 788s SNPs introduced: 10 788s Reference gaps introduced: 1 788s Read gaps introduced: 0 788s Rearrangements introduced: 0 788s Created read sampler 788s Sampling 89 reads 788s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 788s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 788s parsing sequence Sim.pm.1... 788s parsing sequence Sim.pm.2... 788s Parsed 86 reference bases 788s *** Run 59 of 100 788s /usr/bin/bowtie2 --cp-min 3 --trim5 4 --cp-ival 4 --local -N 0 -L14 --mp 8.70221447883557,5.0085312056938 -a --mm --gbar 15 --rdg 25.0608935608417,14.1818858759759 --score-min L,3.0657468859984,8.58444224282987 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 788s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '2' because it was < 2 characters long 788s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '9' because it was < 2 characters long 788s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 788s Warning: skipping read '14' because it was < 2 characters long 788s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '22' because it was < 2 characters long 788s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '23' because it was < 2 characters long 788s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '24' because it was < 2 characters long 788s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 788s Warning: skipping read '26' because it was < 2 characters long 788s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '28' because it was < 2 characters long 788s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '32' because it was < 2 characters long 788s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '66' because it was < 2 characters long 788s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '75' because it was < 2 characters long 788s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '77' because it was < 2 characters long 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '83' because it was < 2 characters long 788s Read 50 alignments... 788s 89 reads; of these: 788s 79 (88.76%) were paired; of these: 788s 79 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 79 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 79 pairs aligned 0 times concordantly or discordantly; of these: 788s 158 mates make up the pairs; of these: 788s 158 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 10 (11.24%) were unpaired; of these: 788s 10 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 0.00% overall alignment rate 788s Read 100 alignments... 788s Read 150 alignments... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s /usr/bin/bowtie2 --cp-min 3 --trim5 4 --cp-ival 4 --local -N 0 -L14 --mp 8.70221447883557,5.0085312056938 -a --mm --gbar 15 --rdg 25.0608935608417,14.1818858759759 --score-min L,3.0657468859984,8.58444224282987 -f -p 3 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s Processing line... 788s --- Summary --- 788s Read 1 reference strings 788s Checked 0 alignments, 0 edits 788s --------------- 788s PASSED 788s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 788s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '2' because it was < 2 characters long 788s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '9' because it was < 2 characters long 788s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 788s Warning: skipping read '14' because it was < 2 characters long 788s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '22' because it was < 2 characters long 788s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '23' because it was < 2 characters long 788s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '24' because it was < 2 characters long 788s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 788s Warning: skipping read '26' because it was < 2 characters long 788s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '28' because it was < 2 characters long 788s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '32' because it was < 2 characters long 788s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '66' because it was < 2 characters long 788s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '75' because it was < 2 characters long 788s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '77' because it was < 2 characters long 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '83' because it was < 2 characters long 788s 89 reads; of these: 788s 79 (88.76%) were paired; of these: 788s 79 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 79 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 79 pairs aligned 0 times concordantly or discordantly; of these: 788s 158 mates make up the pairs; of these: 788s 158 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 10 (11.24%) were unpaired; of these: 788s 10 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 0.00% overall alignment rate 788s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 788s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 788s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 788s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 788s /usr/bin/bowtie2 --cp-min 3 --trim5 4 --cp-ival 4 --local -N 0 -L14 --mp 8.70221447883557,5.0085312056938 -a --mm --gbar 15 --rdg 25.0608935608417,14.1818858759759 --score-min L,3.0657468859984,8.58444224282987 -f -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 788s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '2' because it was < 2 characters long 788s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '9' because it was < 2 characters long 788s Warning: skipping read '14' because length (1) <= # seed mismatches (0) 788s Warning: skipping read '14' because it was < 2 characters long 788s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '22' because it was < 2 characters long 788s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '23' because it was < 2 characters long 788s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '24' because it was < 2 characters long 788s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 788s Warning: skipping read '26' because it was < 2 characters long 788s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '28' because it was < 2 characters long 788s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '32' because it was < 2 characters long 788s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '66' because it was < 2 characters long 788s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '75' because it was < 2 characters long 788s Warning: skipping mate #2 of read '77' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '77' because it was < 2 characters long 788s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (0) 788s Warning: skipping mate #1 of read '79' because it was < 2 characters long 788s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 788s Warning: skipping mate #2 of read '83' because it was < 2 characters long 788s 89 reads; of these: 788s 79 (88.76%) were paired; of these: 788s 79 (100.00%) aligned concordantly 0 times 788s 0 (0.00%) aligned concordantly exactly 1 time 788s 0 (0.00%) aligned concordantly >1 times 788s ---- 788s 79 pairs aligned concordantly 0 times; of these: 788s 0 (0.00%) aligned discordantly 1 time 788s ---- 788s 79 pairs aligned 0 times concordantly or discordantly; of these: 788s 158 mates make up the pairs; of these: 788s 158 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 10 (11.24%) were unpaired; of these: 788s 10 (100.00%) aligned 0 times 788s 0 (0.00%) aligned exactly 1 time 788s 0 (0.00%) aligned >1 times 788s 0.00% overall alignment rate 788s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 788s Flattened IUPAC characters 788s Mutating sequence Sim.pm.1 788s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutating sequence Sim.pm.2 788s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 788s Finished SNPs 788s Finished ref gaps 788s Finished read gaps 788s Mutated reference genome to subject genome 788s SNPs introduced: 12 788s Reference gaps introduced: 0 788s Read gaps introduced: 0 788s Rearrangements introduced: 1 788s Created read sampler 788s Sampling 68 reads 788s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 788s *** Run 60 of 100 788s /usr/bin/bowtie2 --rdg 46.0836555087523,18.9861544164937 --rfg 46.3036582026682,16.1403287811801 --score-min L,8.84820436783944,7.70003132312683 --mm --mp 7.49298968580744,1.1798516517912 --cp-ival 1 -D 10 --n-ceil 0.659662503549509,1.02213806653476 --trim5 5 --ma 35.3009589112278 --cp-min 4 -R 3 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 788s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 788s parsing sequence Sim.pm.1... 788s parsing sequence Sim.pm.2... 788s Parsed 86 reference bases 788s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 789s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 789s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '1' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 789s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '5' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 789s Warning: skipping read '8' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '8' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 789s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '20' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 789s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '23' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 789s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '25' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 789s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '32' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 789s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '34' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 789s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '36' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 789s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '42' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 789s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '46' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 789s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '63' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 789s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '65' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 789s 68 reads; of these: 789s 68 (100.00%) were unpaired; of these: 789s 56 (82.35%) aligned 0 times 789s 6 (8.82%) aligned exactly 1 time 789s 6 (8.82%) aligned >1 times 789s 17.65% overall alignment rate 789s Read 50 alignments... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s GC 789s GC 789s Processing line... 789s CAAC 789s CAAC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s AG 789s AG 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s TC 789s TC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s AACGG 789s AACGG 789s Processing line... 789s Processing line... 789s *** Run 61 of 100 789s /usr/bin/bowtie2 -a --mm --score-min L,6.87843546535215,9.9754000687548 --rfg 13.4250844722298,17.1297548026914 --mp 6.75595037418221,4.96752605365576 --cp-ival 1 --norc --np 1 -R 1 --ma 3.78286665423944 --cp-min 3 --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s CACC 789s CACC 789s Processing line... 789s TTTCC 789s TTTCC 789s Processing line... 789s CC 789s CC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s CTG 789s CTG 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s TGTGC 789s TGTGC 789s Processing line... 789s Processing line... 789s ACCCT 789s ACCCT 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s CTTT 789s CTTT 789s Processing line... 789s Processing line... 789s --- Summary --- 789s Read 1 reference strings 789s Checked 12 alignments, 0 edits 789s --------------- 789s PASSED 789s Flattened IUPAC characters 789s Mutating sequence Sim.pm.1 789s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutating sequence Sim.pm.2 789s Introducing 5 SNPs, 2/0 ref/read gaps, and 2 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutated reference genome to subject genome 789s SNPs introduced: 6 789s Reference gaps introduced: 2 789s Read gaps introduced: 0 789s Rearrangements introduced: 2 789s Created read sampler 789s Sampling 8 reads 789s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 789s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 789s parsing sequence Sim.pm.1... 789s parsing sequence Sim.pm.2... 789s Parsed 86 reference bases 789s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 789s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 789s 8 reads; of these: 789s 8 (100.00%) were unpaired; of these: 789s 7 (87.50%) aligned 0 times 789s 1 (12.50%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 12.50% overall alignment rate 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s TGA 789s TGA 789s Processing line... 789s Processing line... 789s Processing line... 789s --- Summary --- 789s Read 1 reference strings 789s Checked 1 alignments, 0 edits 789s /usr/bin/bowtie2 -a --mm --score-min L,6.87843546535215,9.9754000687548 --rfg 13.4250844722298,17.1297548026914 --mp 6.75595037418221,4.96752605365576 --cp-ival 1 --norc --np 1 -R 1 --ma 3.78286665423944 --cp-min 3 --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 789s --------------- 789s PASSED 789s ALSO checking that bowtie2 and bowtie2-align match up 789s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 789s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 789s 8 reads; of these: 789s 8 (100.00%) were unpaired; of these: 789s 7 (87.50%) aligned 0 times 789s 1 (12.50%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 12.50% overall alignment rate 789s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 789s /usr/bin/bowtie2 -a --mm --score-min L,6.87843546535215,9.9754000687548 --rfg 13.4250844722298,17.1297548026914 --mp 6.75595037418221,4.96752605365576 --cp-ival 1 --norc --np 1 -R 1 --ma 3.78286665423944 --cp-min 3 --qseq -p 2 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 789s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 789s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 789s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 789s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 789s 8 reads; of these: 789s 8 (100.00%) were unpaired; of these: 789s 7 (87.50%) aligned 0 times 789s 1 (12.50%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 12.50% overall alignment rate 789s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 789s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 789s Flattened IUPAC characters 789s Mutating sequence Sim.pm.1 789s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutating sequence Sim.pm.2 789s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutated reference genome to subject genome 789s SNPs introduced: 2 789s Reference gaps introduced: 0 789s Read gaps introduced: 0 789s Rearrangements introduced: 1 789s Created read sampler 789s Sampling 58 reads 789s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 789s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 789s parsing sequence Sim.pm.1... 789s parsing sequence Sim.pm.2... 789s Parsed 86 reference bases 789s *** Run 62 of 100 789s /usr/bin/bowtie2 --n-ceil 0.163047746456721,0.795511232977014 --cp-ival 1 --cp-min 3 --mp 8.34333743396387,5.71312418981248 --ma 30.2142429962804 --rdg 23.6784255465801,17.7316420288708 --norc --score-min L,8.62789617216735,7.10243128785242 --trim5 7 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 789s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 789s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 789s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '6' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 789s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '8' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 789s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '14' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 789s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '19' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 789s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '21' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 789s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '30' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 789s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '35' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 789s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '40' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 789s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '41' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 789s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '43' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 789s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '46' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 789s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '47' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 789s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '51' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 789s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '56' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 789s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '58' because it was < 2 characters long 789s 58 reads; of these: 789s 58 (100.00%) were unpaired; of these: 789s 51 (87.93%) aligned 0 times 789s 5 (8.62%) aligned exactly 1 time 789s 2 (3.45%) aligned >1 times 789s 12.07% overall alignment rate 789s Read 50 alignments... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s AATCA 789s AATCA 789s Processing line... 789s Processing line... 789s TC 789s TC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s TGCAATTCGAAT 789s TGCAATTCGAAT 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s TGCAA 789s TGCAA 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s GAG 789s GAG 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s CGC 789s CGC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s AATCA 789s AATCA 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s --- Summary --- 789s Read 1 reference strings 789s Checked 7 alignments, 0 edits 789s --------------- 789s PASSED 789s Flattened IUPAC characters 789s Mutating sequence Sim.pm.2 789s Introducing 7 SNPs, 1/2 ref/read gaps, and 2 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutating sequence Sim.pm.1 789s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutated reference genome to subject genome 789s SNPs introduced: 9 789s Reference gaps introduced: 2 789s Read gaps introduced: 2 789s Rearrangements introduced: 2 789s Created read sampler 789s Sampling 114 reads 789s *** Run 63 of 100 789s /usr/bin/bowtie2 --nofw --mp 4.80796066609987,4.58384685154398 --local --cp-ival 2 --trim3 4 --score-min L,6.19647022183052,1.46901739429053 --rfg 32.3350643806534,18.7430002080067 --rdg 46.4112309450072,17.6431988513432 --gbar 1 --cp-min 2 --np 4 -M 10 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 789s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 789s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 789s parsing sequence Sim.pm.1... 789s parsing sequence Sim.pm.2... 789s Parsed 86 reference bases 789s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 789s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 789s Read 50 alignments... 789s Read 100 alignments... 789s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 789s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 789s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 789s Read 150 alignments... 789s 114 reads; of these: 789s 105 (92.11%) were paired; of these: 789s 105 (100.00%) aligned concordantly 0 times 789s 0 (0.00%) aligned concordantly exactly 1 time 789s 0 (0.00%) aligned concordantly >1 times 789s ---- 789s 105 pairs aligned concordantly 0 times; of these: 789s 0 (0.00%) aligned discordantly 1 time 789s ---- 789s 105 pairs aligned 0 times concordantly or discordantly; of these: 789s 210 mates make up the pairs; of these: 789s 210 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 9 (7.89%) were unpaired; of these: 789s 9 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 0.00% overall alignment rate 789s Read 200 alignments... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s --- Summary --- 789s Read 1 reference strings 789s Checked 0 alignments, 0 edits 789s --------------- 789s PASSED 789s ALSO checking that bowtie2 and bowtie2-align match up 789s /usr/bin/bowtie2 --nofw --mp 4.80796066609987,4.58384685154398 --local --cp-ival 2 --trim3 4 --score-min L,6.19647022183052,1.46901739429053 --rfg 32.3350643806534,18.7430002080067 --rdg 46.4112309450072,17.6431988513432 --gbar 1 --cp-min 2 --np 4 -M 10 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 789s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 789s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 789s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #2 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 789s Warning: skipping read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 789s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 789s 114 reads; of these: 789s 105 (92.11%) were paired; of these: 789s 105 (100.00%) aligned concordantly 0 times 789s 0 (0.00%) aligned concordantly exactly 1 time 789s 0 (0.00%) aligned concordantly >1 times 789s ---- 789s 105 pairs aligned concordantly 0 times; of these: 789s 0 (0.00%) aligned discordantly 1 time 789s ---- 789s 105 pairs aligned 0 times concordantly or discordantly; of these: 789s 210 mates make up the pairs; of these: 789s 210 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 9 (7.89%) were unpaired; of these: 789s 9 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 0.00% overall alignment rate 789s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 789s Flattened IUPAC characters 789s Mutating sequence Sim.pm.1 789s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutating sequence Sim.pm.2 789s Introducing 8 SNPs, 4/0 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutated reference genome to subject genome 789s SNPs introduced: 8 789s Reference gaps introduced: 5 789s Read gaps introduced: 1 789s Rearrangements introduced: 0 789s Created read sampler 789s Sampling 79 reads 789s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 789s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 789s parsing sequence Sim.pm.1... 789s parsing sequence Sim.pm.2... 789s Parsed 86 reference bases 789s *** Run 64 of 100 789s /usr/bin/bowtie2 --mm --score-min L,7.03662552503551,3.67079059640747 --rfg 9.61608612368224,16.2404541682632 --trim3 6 --local --cp-ival 2 -D 12 --np 7 --norc --cp-min 7 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 789s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '3' because it was < 2 characters long 789s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '7' because it was < 2 characters long 789s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '8' because it was < 2 characters long 789s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '9' because it was < 2 characters long 789s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '17' because it was < 2 characters long 789s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '19' because it was < 2 characters long 789s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '22' because it was < 2 characters long 789s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '31' because it was < 2 characters long 789s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '34' because it was < 2 characters long 789s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '37' because it was < 2 characters long 789s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '52' because it was < 2 characters long 789s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '53' because it was < 2 characters long 789s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '58' because it was < 2 characters long 789s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '66' because it was < 2 characters long 789s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '67' because it was < 2 characters long 789s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '69' because it was < 2 characters long 789s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '70' because it was < 2 characters long 789s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '74' because it was < 2 characters long 789s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '75' because it was < 2 characters long 789s 79 reads; of these: 789s 65 (82.28%) were paired; of these: 789s 65 (100.00%) aligned concordantly 0 times 789s 0 (0.00%) aligned concordantly exactly 1 time 789s 0 (0.00%) aligned concordantly >1 times 789s ---- 789s 65 pairs aligned concordantly 0 times; of these: 789s 0 (0.00%) aligned discordantly 1 time 789s ---- 789s 65 pairs aligned 0 times concordantly or discordantly; of these: 789s 130 mates make up the pairs; of these: 789s 130 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 14 (17.72%) were unpaired; of these: 789s 14 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 0.00% overall alignment rate 789s Read 50 alignments... 789s Read 100 alignments... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s --- Summary --- 789s Read 1 reference strings 789s Checked 0 alignments, 0 edits 789s --------------- 789s PASSED 789s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 789s /usr/bin/bowtie2 --mm --score-min L,7.03662552503551,3.67079059640747 --rfg 9.61608612368224,16.2404541682632 --trim3 6 --local --cp-ival 2 -D 12 --np 7 --norc --cp-min 7 -f -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 789s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '3' because it was < 2 characters long 789s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '7' because it was < 2 characters long 789s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '8' because it was < 2 characters long 789s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '9' because it was < 2 characters long 789s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '17' because it was < 2 characters long 789s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '19' because it was < 2 characters long 789s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '22' because it was < 2 characters long 789s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '31' because it was < 2 characters long 789s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '34' because it was < 2 characters long 789s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '37' because it was < 2 characters long 789s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '52' because it was < 2 characters long 789s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '53' because it was < 2 characters long 789s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '58' because it was < 2 characters long 789s Warning: skipping mate #1 of read '66' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '66' because it was < 2 characters long 789s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '67' because it was < 2 characters long 789s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '69' because it was < 2 characters long 789s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 789s Warning: skipping read '70' because it was < 2 characters long 789s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '74' because it was < 2 characters long 789s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '75' because it was < 2 characters long 789s 79 reads; of these: 789s 65 (82.28%) were paired; of these: 789s 65 (100.00%) aligned concordantly 0 times 789s 0 (0.00%) aligned concordantly exactly 1 time 789s 0 (0.00%) aligned concordantly >1 times 789s ---- 789s 65 pairs aligned concordantly 0 times; of these: 789s 0 (0.00%) aligned discordantly 1 time 789s ---- 789s 65 pairs aligned 0 times concordantly or discordantly; of these: 789s 130 mates make up the pairs; of these: 789s 130 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 14 (17.72%) were unpaired; of these: 789s 14 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 0.00% overall alignment rate 789s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 789s Flattened IUPAC characters 789s Mutating sequence Sim.pm.1 789s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutating sequence Sim.pm.2 789s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutated reference genome to subject genome 789s SNPs introduced: 10 789s Reference gaps introduced: 0 789s Read gaps introduced: 0 789s Rearrangements introduced: 1 789s Created read sampler 789s Sampling 48 reads 789s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 789s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 789s parsing sequence Sim.pm.1... 789s parsing sequence Sim.pm.2... 789s Parsed 86 reference bases 789s *** Run 65 of 100 789s /usr/bin/bowtie2 --norc --np 5 --trim5 5 --cp-min 2 -R 1 --score-min L,4.6684280698264,4.44836116401046 --rdg 37.1785191731407,12.4385441170429 --gbar 3 --mm --nofw --mp 8.32619105173566,3.69852336886082 -N 0 -L24 --cp-ival 2 --n-ceil 0.972703343806688,1.24074336116351 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 789s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '3' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 789s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '11' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 789s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '12' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 789s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #2 of read '15' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 789s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '21' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 789s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '37' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 789s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '39' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 789s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '41' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 789s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '42' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 789s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '46' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 789s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '47' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 789s 48 reads; of these: 789s 45 (93.75%) were paired; of these: 789s 45 (100.00%) aligned concordantly 0 times 789s 0 (0.00%) aligned concordantly exactly 1 time 789s 0 (0.00%) aligned concordantly >1 times 789s ---- 789s 45 pairs aligned concordantly 0 times; of these: 789s 0 (0.00%) aligned discordantly 1 time 789s ---- 789s 45 pairs aligned 0 times concordantly or discordantly; of these: 789s 90 mates make up the pairs; of these: 789s 90 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 3 (6.25%) were unpaired; of these: 789s 3 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 0.00% overall alignment rate 789s Read 50 alignments... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s --- Summary --- 789s Read 1 reference strings 789s Checked 0 alignments, 0 edits 789s --------------- 789s PASSED 789s ALSO checking that bowtie2 and bowtie2-align match up 789s /usr/bin/bowtie2 --norc --np 5 --trim5 5 --cp-min 2 -R 1 --score-min L,4.6684280698264,4.44836116401046 --rdg 37.1785191731407,12.4385441170429 --gbar 3 --mm --nofw --mp 8.32619105173566,3.69852336886082 -N 0 -L24 --cp-ival 2 --n-ceil 0.972703343806688,1.24074336116351 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 789s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '3' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 789s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '11' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 789s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '12' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 789s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #2 of read '15' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 789s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '21' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 789s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '37' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 789s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '39' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 789s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '41' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 789s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '42' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 789s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '46' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 789s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '47' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 789s 48 reads; of these: 789s 45 (93.75%) were paired; of these: 789s 45 (100.00%) aligned concordantly 0 times 789s 0 (0.00%) aligned concordantly exactly 1 time 789s 0 (0.00%) aligned concordantly >1 times 789s ---- 789s 45 pairs aligned concordantly 0 times; of these: 789s 0 (0.00%) aligned discordantly 1 time 789s ---- 789s 45 pairs aligned 0 times concordantly or discordantly; of these: 789s 90 mates make up the pairs; of these: 789s 90 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 3 (6.25%) were unpaired; of these: 789s 3 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 0.00% overall alignment rate 789s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 789s /usr/bin/bowtie2 --norc --np 5 --trim5 5 --cp-min 2 -R 1 --score-min L,4.6684280698264,4.44836116401046 --rdg 37.1785191731407,12.4385441170429 --gbar 3 --mm --nofw --mp 8.32619105173566,3.69852336886082 -N 0 -L24 --cp-ival 2 --n-ceil 0.972703343806688,1.24074336116351 -f -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 789s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 789s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '3' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 789s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '11' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 789s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '12' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 789s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #2 of read '15' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 789s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '21' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 789s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '37' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 789s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '39' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 789s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '41' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 789s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '42' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 789s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '46' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 789s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '47' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 789s 48 reads; of these: 789s 45 (93.75%) were paired; of these: 789s 45 (100.00%) aligned concordantly 0 times 789s 0 (0.00%) aligned concordantly exactly 1 time 789s 0 (0.00%) aligned concordantly >1 times 789s ---- 789s 45 pairs aligned concordantly 0 times; of these: 789s 0 (0.00%) aligned discordantly 1 time 789s ---- 789s 45 pairs aligned 0 times concordantly or discordantly; of these: 789s 90 mates make up the pairs; of these: 789s 90 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 3 (6.25%) were unpaired; of these: 789s 3 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 0.00% overall alignment rate 789s Flattened IUPAC characters 789s Mutating sequence Sim.pm.1 789s Introducing 1 SNPs, 1/0 ref/read gaps, and 1 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 789s Mutating sequence Sim.pm.2 789s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutated reference genome to subject genome 789s SNPs introduced: 5 789s Reference gaps introduced: 1 789s Read gaps introduced: 1 789s Rearrangements introduced: 1 789s Created read sampler 789s Sampling 88 reads 789s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 789s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 789s parsing sequence Sim.pm.1... 789s parsing sequence Sim.pm.2... 789s Parsed 86 reference bases 789s *** Run 66 of 100 789s /usr/bin/bowtie2 --nofw --ma 26.0337286283574 --mp 8.66126117725261,6.61268038771946 -N 1 -L30 --cp-min 3 -D 23 --cp-ival 1 --mm --score-min L,7.10134852613072,3.34847694850552 --rfg 41.8520132384361 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 789s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 789s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 789s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 789s Warning: skipping read '8' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 789s Warning: skipping read '26' because length (1) <= # seed mismatches (1) 789s Warning: skipping read '26' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 789s Warning: skipping read '57' because length (1) <= # seed mismatches (1) 789s Warning: skipping read '57' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 789s Warning: skipping read '81' because length (1) <= # seed mismatches (1) 789s Warning: skipping read '81' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 789s 88 reads; of these: 789s 88 (100.00%) were unpaired; of these: 789s 77 (87.50%) aligned 0 times 789s 7 (7.95%) aligned exactly 1 time 789s 4 (4.55%) aligned >1 times 789s 12.50% overall alignment rate 789s Read 50 alignments... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s GGAGG 789s GGAGG 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s GGC 789s GGC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s GCAATTCGAATCATGACTGG 789s GCAATTCGAATCATGACTGG 789s Processing line... 789s GATCTCAAAT 789s GATCTCAAAT 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s GTGCAATT 789s GTGCAATT 789s Processing line... 789s TGGATCTCAAA 789s TGGATCTCAAA 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s GCAATTCGAATC 789s GCAATTCGAATC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s CA 789s CA 789s Processing line... 789s GAC 789s GAC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s CCC 789s CCC 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s CAAT 789s CAAT 789s --- Summary --- 789s Read 1 reference strings 789s Checked 11 alignments, 0 edits 789s --------------- 789s PASSED 789s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 789s /usr/bin/bowtie2 --nofw --ma 26.0337286283574 --mp 8.66126117725261,6.61268038771946 -N 1 -L30 --cp-min 3 -D 23 --cp-ival 1 --mm --score-min L,7.10134852613072,3.34847694850552 --rfg 41.8520132384361 -f -p 3 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 789s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 789s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 789s Warning: skipping read '8' because length (1) <= # seed mismatches (1) 789s Warning: skipping read '8' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 789s Warning: skipping read '26' because length (1) <= # seed mismatches (1) 789s Warning: skipping read '26' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 789s Warning: skipping read '57' because length (1) <= # seed mismatches (1) 789s Warning: skipping read '57' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 789s Warning: skipping read '81' because length (1) <= # seed mismatches (1) 789s Warning: skipping read '81' because it was < 2 characters long 789s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 789s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 789s 88 reads; of these: 789s 88 (100.00%) were unpaired; of these: 789s 77 (87.50%) aligned 0 times 789s 7 (7.95%) aligned exactly 1 time 789s 4 (4.55%) aligned >1 times 789s 12.50% overall alignment rate 789s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 789s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 789s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 789s Flattened IUPAC characters 789s Mutating sequence Sim.pm.1 789s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutating sequence Sim.pm.2 789s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 789s Finished SNPs 789s Finished ref gaps 789s Finished read gaps 789s Mutated reference genome to subject genome 789s SNPs introduced: 8 789s Reference gaps introduced: 0 789s Read gaps introduced: 0 789s Rearrangements introduced: 0 789s Created read sampler 789s Sampling 73 reads 789s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 789s *** Run 67 of 100 789s /usr/bin/bowtie2 --score-min L,8.93757146862036,1.12942048348521 --rfg 20.0877067444171 --mm --local --cp-ival 1 --mp 5.89924145696476,1.65866687520718 --norc --trim5 4 -M 3 --cp-min 2 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 789s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 789s parsing sequence Sim.pm.1... 789s parsing sequence Sim.pm.2... 789s Parsed 86 reference bases 789s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 789s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 789s Warning: skipping read '6' because it was < 2 characters long 789s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '13' because it was < 2 characters long 789s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '17' because it was < 2 characters long 789s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '20' because it was < 2 characters long 789s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '48' because it was < 2 characters long 789s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '55' because it was < 2 characters long 789s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 789s Warning: skipping mate #1 of read '61' because it was < 2 characters long 789s Read 50 alignments... 789s 73 reads; of these: 789s 68 (93.15%) were paired; of these: 789s 68 (100.00%) aligned concordantly 0 times 789s 0 (0.00%) aligned concordantly exactly 1 time 789s 0 (0.00%) aligned concordantly >1 times 789s ---- 789s 68 pairs aligned concordantly 0 times; of these: 789s 0 (0.00%) aligned discordantly 1 time 789s ---- 789s 68 pairs aligned 0 times concordantly or discordantly; of these: 789s 136 mates make up the pairs; of these: 789s 135 (99.26%) aligned 0 times 789s 1 (0.74%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 5 (6.85%) were unpaired; of these: 789s 5 (100.00%) aligned 0 times 789s 0 (0.00%) aligned exactly 1 time 789s 0 (0.00%) aligned >1 times 789s 0.71% overall alignment rate 789s Read 100 alignments... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s TGTGCAATTCGAATCATGACT 789s TGTGCAATTCGAATCATGACT 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s /usr/bin/bowtie2 --score-min L,8.93757146862036,1.12942048348521 --rfg 20.0877067444171 --mm --local --cp-ival 1 --mp 5.89924145696476,1.65866687520718 --norc --trim5 4 -M 3 --cp-min 2 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s Processing line... 789s --- Summary --- 789s Read 1 reference strings 789s Checked 1 alignments, 0 edits 789s --------------- 789s PASSED 789s ALSO checking that bowtie2 and bowtie2-align match up 789s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 790s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '6' because it was < 2 characters long 790s Warning: skipping mate #1 of read '13' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '13' because it was < 2 characters long 790s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '17' because it was < 2 characters long 790s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '20' because it was < 2 characters long 790s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '48' because it was < 2 characters long 790s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '55' because it was < 2 characters long 790s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '61' because it was < 2 characters long 790s 73 reads; of these: 790s 68 (93.15%) were paired; of these: 790s 68 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 68 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 68 pairs aligned 0 times concordantly or discordantly; of these: 790s 136 mates make up the pairs; of these: 790s 135 (99.26%) aligned 0 times 790s 1 (0.74%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 5 (6.85%) were unpaired; of these: 790s 5 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 0.71% overall alignment rate 790s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.2 790s Introducing 4 SNPs, 3/0 ref/read gaps, and 2 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.1 790s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 9 790s Reference gaps introduced: 3 790s Read gaps introduced: 0 790s Rearrangements introduced: 2 790s Created read sampler 790s Sampling 138 reads 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s *** Run 68 of 100 790s /usr/bin/bowtie2 --cp-ival 1 --cp-min 2 --score-min L,6.95663414910152,6.51477061014413 --gbar 4 --np 2 -a -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 790s parsing sequence Sim.pm.2... 790s Parsed 86 reference bases 790s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 790s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '19' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 790s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '24' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 790s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '48' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 790s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '52' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 790s Warning: skipping read '84' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '84' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 790s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '89' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 790s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '93' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 790s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '96' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 790s Warning: skipping read '125' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '125' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 790s Warning: skipping read '136' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '136' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 790s Warning: skipping read '137' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '137' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 790s Read 50 alignments... 790s 138 reads; of these: 790s 138 (100.00%) were unpaired; of these: 790s 111 (80.43%) aligned 0 times 790s 15 (10.87%) aligned exactly 1 time 790s 12 (8.70%) aligned >1 times 790s 19.57% overall alignment rate 790s Read 100 alignments... 790s Read 150 alignments... 790s Read 200 alignments... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TCGA 790s TCGA 790s Processing line... 790s TCGA 790s TCGA 790s Processing line... 790s Processing line... 790s GA 790s GA 790s Processing line... 790s TC 790s TC 790s Processing line... 790s TC 790s TC 790s Processing line... 790s TC 790s TC 790s Processing line... 790s TC 790s TC 790s Processing line... 790s TC 790s TC 790s Processing line... 790s TC 790s TC 790s Processing line... 790s GA 790s GA 790s Processing line... 790s TC 790s TC 790s Processing line... 790s GA 790s GA 790s Processing line... 790s GA 790s GA 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AGGGCCAC 790s AGGGCCAC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CTGGATCT 790s CTGGATCT 790s Processing line... 790s Processing line... 790s Processing line... 790s TTCGAATCATGACTGGATCT 790s TTCGAATCATGACTGGATCT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TG 790s TG 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s TG 790s TG 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s TG 790s TG 790s Processing line... 790s TG 790s TG 790s Processing line... 790s CA 790s CA 790s Processing line... 790s Processing line... 790s TCCCG 790s TCCCG 790s Processing line... 790s CGGGA 790s CGGGA 790s /usr/bin/bowtie2 --cp-ival 1 --cp-min 2 --score-min L,6.95663414910152,6.51477061014413 --gbar 4 --np 2 -a -q -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AAGGGCCA 790s AAGGGCCA 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AGGGC 790s AGGGC 790s Processing line... 790s GAATCATGACT 790s GAATCATGACT 790s Processing line... 790s Processing line... 790s CGAA 790s CGAA 790s Processing line... 790s TTCG 790s TTCG 790s Processing line... 790s CAACGG 790s CAACGG 790s Processing line... 790s ACTGGAT 790s ACTGGAT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AC 790s AC 790s Processing line... 790s AC 790s AC 790s Processing line... 790s AC 790s AC 790s Processing line... 790s AC 790s AC 790s Processing line... 790s GT 790s GT 790s Processing line... 790s AC 790s AC 790s Processing line... 790s Processing line... 790s CCACCG 790s CCACCG 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TCAT 790s TCAT 790s Processing line... 790s ATGA 790s ATGA 790s Processing line... 790s CAATTCGAAT 790s CAATTCGAAT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TGCAATTCGAA 790s TGCAATTCGAA 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AGGGC 790s AGGGC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TCCCG 790s TCCCG 790s Processing line... 790s CGGGA 790s CGGGA 790s Processing line... 790s Processing line... 790s CGCC 790s CGCC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CTGG 790s CTGG 790s Processing line... 790s Processing line... 790s Processing line... 790s GG 790s GG 790s Processing line... 790s GG 790s GG 790s Processing line... 790s GG 790s GG 790s Processing line... 790s CC 790s CC 790s Processing line... 790s CC 790s CC 790s Processing line... 790s GG 790s GG 790s Processing line... 790s CC 790s CC 790s Processing line... 790s CC 790s CC 790s Processing line... 790s CC 790s CC 790s Processing line... 790s CC 790s CC 790s Processing line... 790s GG 790s GG 790s Processing line... 790s CC 790s CC 790s Processing line... 790s GG 790s GG 790s Processing line... 790s CC 790s CC 790s Processing line... 790s GG 790s GG 790s Processing line... 790s CC 790s CC 790s Processing line... 790s Processing line... 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s TG 790s TG 790s Processing line... 790s TG 790s TG 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s TG 790s TG 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s CA 790s CA 790s Processing line... 790s TG 790s TG 790s Processing line... 790s Processing line... 790s CTGGAT 790s CTGGAT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CAC 790s CAC 790s Processing line... 790s GTG 790s GTG 790s Processing line... 790s CAC 790s CAC 790s Processing line... 790s CAC 790s CAC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s GCCACC 790s GCCACC 790s Processing line... 790s GCCACC 790s GCCACC 790s Processing line... 790s Processing line... 790s Processing line... 790s --- Summary --- 790s Read 1 reference strings 790s Checked 88 alignments, 0 edits 790s --------------- 790s PASSED 790s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 790s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 790s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '19' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 790s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '24' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 790s Warning: skipping read '48' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '48' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 790s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '52' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 790s Warning: skipping read '84' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '84' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 790s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '89' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 790s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '93' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 790s Warning: skipping read '96' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '96' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 790s Warning: skipping read '125' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '125' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 790s Warning: skipping read '136' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '136' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 790s Warning: skipping read '137' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '137' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 790s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 790s 138 reads; of these: 790s 138 (100.00%) were unpaired; of these: 790s 111 (80.43%) aligned 0 times 790s 15 (10.87%) aligned exactly 1 time 790s 12 (8.70%) aligned >1 times 790s 19.57% overall alignment rate 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.1 790s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.2 790s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 12 790s Reference gaps introduced: 0 790s Read gaps introduced: 1 790s Rearrangements introduced: 0 790s Created read sampler 790s Sampling 76 reads 790s *** Run 69 of 100 790s /usr/bin/bowtie2 --ma 7.5826576564116 --cp-min 2 --norc --np 10 -i C,2.66557135925329 -k 3 --mp 5.37801543629324,1.53445223692266 --nofw --cp-ival 1 -D 8 --rdg 21.6167120516396,7.28280311824673 --score-min L,2.45362591117537,1.64135500486716 --mm -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s parsing sequence Sim.pm.2... 790s Parsed 86 reference bases 790s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 790s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 790s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '18' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 790s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '36' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 790s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '65' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 790s 76 reads; of these: 790s 76 (100.00/usr/bin/bowtie2 --ma 7.5826576564116 --cp-min 2 --norc --np 10 -i C,2.66557135925329 -k 3 --mp 5.37801543629324,1.53445223692266 --nofw --cp-ival 1 -D 8 --rdg 21.6167120516396,7.28280311824673 --score-min L,2.45362591117537,1.64135500486716 --mm -q -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 790s %) were unpaired; of these: 790s 76 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 0.00% overall alignment rate 790s Read 50 alignments... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s --- Summary --- 790s Read 1 reference strings 790s Checked 0 alignments, 0 edits 790s --------------- 790s PASSED 790s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 790s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 790s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 790s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '18' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 790s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '36' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 790s Warning: skipping read '65' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '65' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 790s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 790s 76 reads; of these: 790s 76 (100.00%) were unpaired; of these: 790s 76 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 0.00% overall alignment rate 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.1 790s Introducing 5 SNPs, 2/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.2 790s Introducing 14 SNPs, 1/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 19 790s Reference gaps introduced: 3 790s Read gaps introduced: 0 790s Rearrangements introduced: 0 790s Created read sampler 790s Sampling 52 reads 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s parsing sequence Sim.pm.2... 790s *** Run 70 of 100 790s /usr/bin/bowtie2 -N 0 -L15 --rfg 8.28971330524685 --score-min L,4.54793481648642,4.68491507704266 --cp-ival 1 --cp-min 5 -i L --trim3 0 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 790s Parsed 86 reference bases 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 790s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 790s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 790s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 790s 52 reads; of these: 790s 52 (100.00%) were paired; of these: 790s 51 (98.08%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 1 (1.92%) aligned concordantly >1 times 790s ---- 790s 51 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 51 pairs aligned 0 times concordantly or discordantly; of these: 790s 102 mates make up the pairs; of these: 790s 87 (85.29%) aligned 0 times 790s 12 (11.76%) aligned exactly 1 time 790s 3 (2.94%) aligned >1 times 790s 16.35% overall alignment rate 790s Read 50 alignments... 790s Read 100 alignments... 790s /usr/bin/bowtie2 -N 0 -L15 --rfg 8.28971330524685 --score-min L,4.54793481648642,4.68491507704266 --cp-ival 1 --cp-min 5 -i L --trim3 0 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s GAATCATGACTG 790s GAATCATGACTG 790s Processing line... 790s Processing line... 790s TGACTGGATCTC 790s TGACTGGATCTC 790s Processing line... 790s Processing line... 790s TGCA 790s TGCA 790s Processing line... 790s CCACCGG 790s CCACCGG 790s Processing line... 790s CACCGG 790s CACCGG 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CTCAAA 790s CTCAAA 790s Processing line... 790s Processing line... 790s CCACCGGGAGGCAC 790s CCACCGGGAGGCAC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AAAGGGCCACCGGGAGGCAC 790s AAAGGGCCACCGGGAGGCAC 790s Processing line... 790s Processing line... 790s AGGGCCACCGGGAG 790s AGGGCCACCGGGAG 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TGTGCAATTCGAATCAT 790s TGTGCAATTCGAATCAT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s GCA 790s GCA 790s Processing line... 790s Processing line... 790s AAAGGGCCACC 790s AAAGGGCCACC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s GGATCTCAA 790s GGATCTCAA 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CAAT 790s CAAT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CCGGGAGGCA 790s CCGGGAGGCA 790s Processing line... 790s Processing line... 790s CACCGG 790s CACCGG 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AT 790s AT 790s Processing line... 790s Processing line... 790s Processing line... 790s --- Summary --- 790s Read 1 reference strings 790s Checked 17 alignments, 0 edits 790s --------------- 790s PASSED 790s ALSO checking that bowtie2 and bowtie2-align match up 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 790s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_9_9_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 790s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_19_19_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 790s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 790s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 790s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 790s 52 reads; of these: 790s 52 (100.00%) were paired; of these: 790s 51 (98.08%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 1 (1.92%) aligned concordantly >1 times 790s ---- 790s 51 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 51 pairs aligned 0 times concordantly or discordantly; of these: 790s 102 mates make up the pairs; of these: 790s 87 (85.29%) aligned 0 times 790s 12 (11.76%) aligned exactly 1 time 790s 3 (2.94%) aligned >1 times 790s 16.35% overall alignment rate 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.2 790s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.1 790s Introducing 1 SNPs, 3/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 6 790s Reference gaps introduced: 3 790s Read gaps introduced: 0 790s Rearrangements introduced: 0 790s Created read sampler 790s Sampling 79 reads 790s *** Run 71 of 100 790s /usr/bin/bowtie2 --trim3 0 --cp-ival 1 --local --cp-min 8 -i L,0.423261570966446 --mm --rfg 19.3077650480718 --score-min L,3.51576631043113,5.49211004089068 --np 1 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s parsing sequence Sim.pm.2... 790s Parsed 86 reference bases 790s Warning: skipping mate #2 of read '3' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '3' because it was < 2 characters long 790s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '16' because it was < 2 characters long 790s Warning: skipping mate #1 of read '31' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '31' because it was < 2 characters long 790s Warning: skipping mate #1 of read '37' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '37' because it was < 2 characters long 790s Warning: skipping mate #1 of read '57' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '57' because it was < 2 characters long 790s Read 50 alignments... 790s 79 reads; of these: 790s 79 (100.00%) were paired; of these: 790s 79 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 79 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 79 pairs aligned 0 times concordantly or discordantly; of these: 790s 158 mates make up the pairs; of these: 790s 158 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 0.00% overall alignment rate 790s Read 100 alignments... 790s Read 150 alignments... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s --- Summary --- 790s Read 1 reference strings 790s Checked 0 alignments, 0 edits 790s --------------- 790s PASSED 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.2 790s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.1 790s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 9 790s Reference gaps introduced: 1 790s Read gaps introduced: 0 790s Rearrangements introduced: 1 790s Created read sampler 790s Sampling 91 reads 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s parsing sequence Sim.pm.2... 790s Parsed 86 reference bases 790s *** Run 72 of 100 790s /usr/bin/bowtie2 --ma 27.7265359949114 --cp-min 5 -R 4 --norc --np 2 --mp 9.97569493154719,1.19354721691996 -D 16 --cp-ival 1 --trim3 3 --rdg 22.8244715617411 --score-min L,4.0635417128918,3.82328865210504 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 790s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 790s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '8' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 790s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '17' because it was < 2 characters long 790s Warning: skipping mate #2 of read '17' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 790s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '24' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 790s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '36' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 790s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '39' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 790s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '43' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 790s Read 50 alignments... 790s Read 100 alignments... 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 790s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '68' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 790s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '75' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 790s 91 reads; of these: 790s 83 (91.21%) were paired; of these: 790s 83 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 83 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 83 pairs aligned 0 times concordantly or discordantly; of these: 790s 166 mates make up the pairs; of these: 790s 155 (93.37%) aligned 0 times 790s 4 (2.41%) aligned exactly 1 time 790s 7 (4.22%) aligned >1 times 790s 8 (8.79%) were unpaired; of these: 790s 7 (87.50%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 1 (12.50%) aligned >1 times 790s 6.90% overall alignment rate 790s Read 150 alignments... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TCCCG 790s TCCCG 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AT 790s AT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s GTGCAATTCG 790s GTGCAATTCG 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AC 790s AC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s GC 790s GC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TCGAATCAT 790s TCGAATCAT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CGG 790s CGG 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TGACT 790s TGACT 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CCG 790s CCG 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s CC 790s CC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s GC 790s GC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s GCC 790s GCC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s --- Summary --- 790s Read 1 reference strings 790s Checked 12 alignments, 0 edits 790s --------------- 790s PASSED 790s ALSO checking that bowtie2 and bowtie2-align match up 790s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 790s /usr/bin/bowtie2 --ma 27.7265359949114 --cp-min 5 -R 4 --norc --np 2 --mp 9.97569493154719,1.19354721691996 -D 16 --cp-ival 1 --trim3 3 --rdg 22.8244715617411 --score-min L,4.0635417128918,3.82328865210504 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 790s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '8' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 790s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '17' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '17' because it was < 2 characters long 790s Warning: skipping mate #2 of read '17' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 790s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '24' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 790s Warning: skipping mate #1 of read '36' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '36' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 790s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '39' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 790s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '43' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 790s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 790s *** Run 73 of 100 790s /usr/bin/bowtie2 --cp-min 7 -k 2 --trim5 3 -i L,0.32510338543625 --np 1 --norc --n-ceil 0.635070783775773,0.765258578838305 --cp-ival 2 --local --nofw --mm --score-min L,6.77412320431344,9.92168044501117 --rfg 11.6992829574454,16.1567595141589 --rdg 16.302139086035,11.9531639600261 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 790s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '68' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 790s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '75' because it was < 2 characters long 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 790s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 790s 91 reads; of these: 790s 83 (91.21%) were paired; of these: 790s 83 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 83 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 83 pairs aligned 0 times concordantly or discordantly; of these: 790s 166 mates make up the pairs; of these: 790s 155 (93.37%) aligned 0 times 790s 4 (2.41%) aligned exactly 1 time 790s 7 (4.22%) aligned >1 times 790s 8 (8.79%) were unpaired; of these: 790s 7 (87.50%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 1 (12.50%) aligned >1 times 790s 6.90% overall alignment rate 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.1 790s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.2 790s Introducing 6 SNPs, 0/0 ref/read gaps, and 3 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 7 790s Reference gaps introduced: 0 790s Read gaps introduced: 1 790s Rearrangements introduced: 3 790s Created read sampler 790s Sampling 74 reads 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s parsing sequence Sim.pm.2... 790s Parsed 86 reference bases 790s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '2' because it was < 2 characters long 790s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '4' because it was < 2 characters long 790s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '14' because it was < 2 characters long 790s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '15' because it was < 2 characters long 790s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '21' because it was < 2 characters long 790s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '28' because it was < 2 characters long 790s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '31' because it was < 2 characters long 790s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '42' because it was < 2 characters long 790s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '43' because it was < 2 characters long 790s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '44' because it was < 2 characters long 790s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '46' because it was < 2 characters long 790s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '54' because it was < 2 characters long 790s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '69' because it was < 2 characters long 790s Warning: skipping mate #2 of read '69' because it was < 2 characters long 790s 74 reads; of these: 790s 67 (90.54%) were paired; of these: 790s 67 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 67 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 67 pairs aligned 0 times concordantly or discordantly; of these: 790s 134 mates make up the pairs; of these: 790s 134 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 7 (9.46%) were unpaired; of these: 790s 7 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 0.00% overall alignment rate 790s Read 50 alignments... 790s Read 100 alignments... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s --- Summary --- 790s Read 1 reference strings 790s Checked 0 alignments, 0 edits 790s --------------- 790s PASSED 790s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 790s /usr/bin/bowtie2 --cp-min 7 -k 2 --trim5 3 -i L,0.32510338543625 --np 1 --norc --n-ceil 0.635070783775773,0.765258578838305 --cp-ival 2 --local --nofw --mm --score-min L,6.77412320431344,9.92168044501117 --rfg 11.6992829574454,16.1567595141589 --rdg 16.302139086035,11.9531639600261 -r -p 2 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 790s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '2' because it was < 2 characters long 790s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '4' because it was < 2 characters long 790s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '14' because it was < 2 characters long 790s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '15' because it was < 2 characters long 790s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '21' because it was < 2 characters long 790s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '28' because it was < 2 characters long 790s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '31' because it was < 2 characters long 790s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '42' because it was < 2 characters long 790s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '43' because it was < 2 characters long 790s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '44' because it was < 2 characters long 790s Warning: skipping mate #1 of read '46' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '46' because it was < 2 characters long 790s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '54' because it was < 2 characters long 790s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #2 of read '69' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '69' because it was < 2 characters long 790s Warning: skipping mate #2 of read '69' because it was < 2 characters long 790s 74 reads; of these: 790s 67 (90.54%) were paired; of these: 790s 67 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 67 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 67 pairs aligned 0 times concordantly or discordantly; of these: 790s 134 mates make up the pairs; of these: 790s 134 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 7 (9.46%) were unpaired; of these: 790s 7 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 0.00% overall alignment rate 790s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 790s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 790s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.2 790s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.1 790s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 7 790s Reference gaps introduced: 0 790s Read gaps introduced: 0 790s Rearrangements introduced: 1 790s Created read sampler 790s Sampling 46 reads 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s parsing sequence Sim.pm.2... 790s Parsed 86 reference bases 790s *** Run 74 of 100 790s /usr/bin/bowtie2 --trim5 9 --np 2 --cp-min 7 --mm --gbar 3 --rdg 6.10947560393504,17.5228328902464 --score-min L,7.94754015772646,1.06905066588396 --trim3 5 --local --cp-ival 1 -N 1 -L28 --nofw -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 790s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 790s Warning: skipping read '1' because it was < 2 characters long 790s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '5' because it was < 2 characters long 790s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '6' because it was < 2 characters long 790s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '7' because it was < 2 characters long 790s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '10' because it was < 2 characters long 790s Warning: skipping mate #1 of read '15' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '15' because it was < 2 characters long 790s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '19' because it was < 2 characters long 790s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '20' because it was < 2 characters long 790s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 790s Warning: skipping read '22' because it was < 2 characters long 790s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '24' because it was < 2 characters long 790s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '29' because it was < 2 characters long 790s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '34' because it was < 2 characters long 790s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (1) 790s Warning: skipping mate #1 of read '37' because it was < 2 characters long 790s 46 reads; of these: 790s 28 (60.87%) were paired; of these: 790s 28 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 28 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 28 pairs aligned 0 times concordantly or discordantly; of these: 790s 56 mates make up the pairs; of these: 790s 52 (92.86%) aligned 0 times 790s 4 (7.14%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 18 (39.13%) were unpaired; of these: 790s 18 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 5.41% overall alignment rate 790s Read 50 alignments... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AATTCGAATCATGACTGGATCTC 790s AATTCGAATCATGACTGGATCTC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TGTGCAATTCGAATCATGACTGGATCTCAAATAAAAGGGCCACCGGGAGGC 790s TGTGCAATTCGAATCATGACTGGATCTCAAATNAAAGGGCCACCGGGAGGC 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s TGTGCAATTCGAATCATGACTGGATCTCAAATGAAAGGGCCACCGGGA 790s TGTGCAATTCGAATCATGACTGGATCTCAAATNAAAGGGCCACCGGGA 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s AAAGGGCCA 790s AAAGGGCCA 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s --- Summary --- 790s Read 1 reference strings 790s Checked 4 alignments, 0 edits 790s --------------- 790s PASSED 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.1 790s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.2 790s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 6 790s Reference gaps introduced: 0 790s Read gaps introduced: 0 790s Rearrangements introduced: 0 790s Created read sampler 790s Sampling 68 reads 790s *** Run 75 of 100 790s /usr/bin/bowtie2 --trim3 2 --mp 9.96155008800875,4.79749509263182 --cp-ival 2 --local -D 12 --rdg 19.1025181639539 --score-min L,5.24323731552585,9.76745805574299 --cp-min 4 -k 10 --norc -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s parsing sequence Sim.pm.2... 790s Parsed 86 reference bases 790s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '4' because it was < 2 characters long 790s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '47' because it was < 2 characters long 790s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '54' because it was < 2 characters long 790s Read 50 alignments... 790s Read 100 alignments... 790s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '68' because it was < 2 characters long 790s 68 reads; of these: 790s 67 (98.53%) were paired; of these: 790s 67 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 67 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 67 pairs aligned 0 times concordantly or discordantly; of these: 790s 134 mates make up the pairs; of these: 790s 134 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 1 (1.47%) were unpaired; of these: 790s 1 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 0.00% overall alignment rate 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s Processing line... 790s --- Summary --- 790s Read 1 reference strings 790s Checked 0 alignments, 0 edits 790s --------------- 790s PASSED 790s ALSO checking that bowtie2 and bowtie2-align match up 790s /usr/bin/bowtie2 --trim3 2 --mp 9.96155008800875,4.79749509263182 --cp-ival 2 --local -D 12 --rdg 19.1025181639539 --score-min L,5.24323731552585,9.76745805574299 --cp-min 4 -k 10 --norc -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 790s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '4' because it was < 2 characters long 790s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '47' because it was < 2 characters long 790s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '54' because it was < 2 characters long 790s Warning: skipping mate #1 of read '68' because length (1) <= # seed mismatches (0) 790s Warning: skipping mate #1 of read '68' because it was < 2 characters long 790s 68 reads; of these: 790s 67 (98.53%) were paired; of these: 790s 67 (100.00%) aligned concordantly 0 times 790s 0 (0.00%) aligned concordantly exactly 1 time 790s 0 (0.00%) aligned concordantly >1 times 790s ---- 790s 67 pairs aligned concordantly 0 times; of these: 790s 0 (0.00%) aligned discordantly 1 time 790s ---- 790s 67 pairs aligned 0 times concordantly or discordantly; of these: 790s 134 mates make up the pairs; of these: 790s 134 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 1 (1.47%) were unpaired; of these: 790s 1 (100.00%) aligned 0 times 790s 0 (0.00%) aligned exactly 1 time 790s 0 (0.00%) aligned >1 times 790s 0.00% overall alignment rate 790s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 790s Flattened IUPAC characters 790s Mutating sequence Sim.pm.1 790s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutating sequence Sim.pm.2 790s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 790s Finished SNPs 790s Finished ref gaps 790s Finished read gaps 790s Mutated reference genome to subject genome 790s SNPs introduced: 7 790s Reference gaps introduced: 2 790s Read gaps introduced: 0 790s Rearrangements introduced: 1 790s Created read sampler 790s Sampling 109 reads 790s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 790s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 790s parsing sequence Sim.pm.1... 790s parsing sequence Sim.pm.2... 790s Parsed 86 reference bases 790s *** Run 76 of 100 790s /usr/bin/bowtie2 --rdg 47.5428306610047,4.76382971644659 --score-min L,1.9074577345205,7.58684070263126 --gbar 2 --mm --trim5 9 --cp-ival 1 --local --cp-min 4 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 790s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '1' because it was < 2 characters long 790s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '2' because it was < 2 characters long 790s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '3' because it was < 2 characters long 790s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '6' because it was < 2 characters long 790s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '18' because it was < 2 characters long 790s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '22' because it was < 2 characters long 790s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '26' because it was < 2 characters long 790s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '29' because it was < 2 characters long 790s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '34' because it was < 2 characters long 790s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '38' because it was < 2 characters long 790s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '41' because it was < 2 characters long 790s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '44' because it was < 2 characters long 790s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '47' because it was < 2 characters long 790s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '49' because it was < 2 characters long 790s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '51' because it was < 2 characters long 790s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '53' because it was < 2 characters long 790s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '58' because it was < 2 characters long 790s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '61' because it was < 2 characters long 790s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '62' because it was < 2 characters long 790s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 790s Warning: skipping read '64' because it was < 2 characters long 790s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '65' because it was < 2 characters long 790s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '66' because it was < 2 characters long 790s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '68' because it was < 2 characters long 790s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '70' because it was < 2 characters long 790s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '85' because it was < 2 characters long 790s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '89' because it was < 2 characters long 790s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '91' because it was < 2 characters long 790s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '93' because it was < 2 characters long 790s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '95' because it was < 2 characters long 790s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '102' because it was < 2 characters long 790s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '104' because it was < 2 characters long 790s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 790s Warning: skipping read '107' because it was < 2 characters long 791s 109 reads; of these: 791s 109 (100.00%) were unpaired; of these: 791s 109 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s Read 50 alignments... 791s Read 100 alignments... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s /usr/bin/bowtie2 --rdg 47.5428306610047,4.76382971644659 --score-min L,1.9074577345205,7.58684070263126 --gbar 2 --mm --trim5 9 --cp-ival 1 --local --cp-min 4 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s --- Summary --- 791s Read 1 reference strings 791s Checked 0 alignments, 0 edits 791s --------------- 791s PASSED 791s ALSO checking that bowtie2 and bowtie2-align match up 791s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '1' because it was < 2 characters long 791s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '2' because it was < 2 characters long 791s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '3' because it was < 2 characters long 791s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '6' because it was < 2 characters long 791s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '18' because it was < 2 characters long 791s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '22' because it was < 2 characters long 791s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '26' because it was < 2 characters long 791s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '29' because it was < 2 characters long 791s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '34' because it was < 2 characters long 791s Warning: skipping read '38' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '38' because it was < 2 characters long 791s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '41' because it was < 2 characters long 791s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '44' because it was < 2 characters long 791s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '47' because it was < 2 characters long 791s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '49' because it was < 2 characters long 791s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '51' because it was < 2 characters long 791s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '53' because it was < 2 characters long 791s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '58' because it was < 2 characters long 791s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '61' because it was < 2 characters long 791s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '62' because it was < 2 characters long 791s Warning: skipping read '64' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '64' because it was < 2 characters long 791s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '65' because it was < 2 characters long 791s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '66' because it was < 2 characters long 791s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '68' because it was < 2 characters long 791s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '70' because it was < 2 characters long 791s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '85' because it was < 2 characters long 791s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '89' because it was < 2 characters long 791s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '91' because it was < 2 characters long 791s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '93' because it was < 2 characters long 791s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '95' because it was < 2 characters long 791s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '102' because it was < 2 characters long 791s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '104' because it was < 2 characters long 791s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '107' because it was < 2 characters long 791s 109 reads; of these: 791s 109 (100.00%) were unpaired; of these: 791s 109 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 791s Flattened IUPAC characters 791s Mutating sequence Sim.pm.2 791s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 791s *** Run 77 of 100 791s /usr/bin/bowtie2 -a --score-min L,8.93238034623318,2.88499221402422 --rdg 20.4484769856187,19.8654127905891 -D 41 --cp-ival 1 --local --nofw --np 5 --norc -R 3 --cp-min 4 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutating sequence Sim.pm.1 791s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutated reference genome to subject genome 791s SNPs introduced: 5 791s Reference gaps introduced: 1 791s Read gaps introduced: 1 791s Rearrangements introduced: 0 791s Created read sampler 791s Sampling 5 reads 791s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 791s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 791s parsing sequence Sim.pm.1... 791s parsing sequence Sim.pm.2... 791s Parsed 86 reference bases 791s 5 reads; of these: 791s 5 (100.00%) were paired; of these: 791s 5 (100.00%) aligned concordantly 0 times 791s 0 (0.00%) aligned concordantly exactly 1 time 791s 0 (0.00%) aligned concordantly >1 times 791s ---- 791s 5 pairs aligned concordantly 0 times; of these: 791s 0 (0.00%) aligned discordantly 1 time 791s ---- 791s 5 pairs aligned 0 times concordantly or discordantly; of these: 791s 10 mates make up the pairs; of these: 791s 10 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s --- Summary --- 791s Read 1 reference strings 791s Checked 0 alignments, 0 edits 791s --------------- 791s PASSED 791s ALSO checking that bowtie2 and bowtie2-align match up 791s /usr/bin/bowtie2 -a --score-min L,8.93238034623318,2.88499221402422 --rdg 20.4484769856187,19.8654127905891 -D 41 --cp-ival 1 --local --nofw --np 5 --norc -R 3 --cp-min 4 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 791s 5 reads; of these: 791s 5 (100.00%) were paired; of these: 791s 5 (100.00%) aligned concordantly 0 times 791s 0 (0.00%) aligned concordantly exactly 1 time 791s 0 (0.00%) aligned concordantly >1 times 791s ---- 791s 5 pairs aligned concordantly 0 times; of these: 791s 0 (0.00%) aligned discordantly 1 time 791s ---- 791s 5 pairs aligned 0 times concordantly or discordantly; of these: 791s 10 mates make up the pairs; of these: 791s 10 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 791s Flattened IUPAC characters 791s Mutating sequence Sim.pm.2 791s Introducing 0 SNPs, 1/0 ref/read gaps, and 1 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutating sequence Sim.pm.1 791s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutated reference genome to subject genome 791s SNPs introduced: 5 791s Reference gaps introduced: 1 791s Read gaps introduced: 0 791s Rearrangements introduced: 1 791s Created read sampler 791s Sampling 63 reads 791s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 791s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 791s parsing sequence Sim.pm.1... 791s parsing sequence Sim.pm.2... 791s Parsed 86 reference bases 791s *** Run 78 of 100 791s /usr/bin/bowtie2 -k 2 --trim5 9 --mm --gbar 3 --np 1 --rdg 18.577388594429,5.22148582564029 --rfg 35.9430075390989,15.3058017836852 --norc --score-min L,8.66491878010244,1.00538006725596 -R 4 --cp-ival 1 --cp-min 2 --nofw --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (1) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (1) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 791s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (0) <= # seed mismatches (0) 791s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 791s 63 reads; of these: 791s 63 (100.00%) were unpaired; of these: 791s 63 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s Read 50 alignments... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s *** Run 79 of 100 791s /usr/bin/bowtie2 --cp-ival 2 --n-ceil 0.180609625928019,0.203931122708202 --local --cp-min 10 --nofw --trim5 7 -M 2 --rdg 40.7969223543715,9.78865881079622 --score-min L,6.1556780539605,7.55898349662945 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s --- Summary --- 791s Read 1 reference strings 791s Checked 0 alignments, 0 edits 791s --------------- 791s PASSED 791s Flattened IUPAC characters 791s Mutating sequence Sim.pm.1 791s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutating sequence Sim.pm.2 791s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutated reference genome to subject genome 791s SNPs introduced: 5 791s Reference gaps introduced: 0 791s Read gaps introduced: 0 791s Rearrangements introduced: 0 791s Created read sampler 791s Sampling 44 reads 791s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 791s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 791s parsing sequence Sim.pm.1... 791s parsing sequence Sim.pm.2... 791s Parsed 86 reference bases 791s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 791s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '6' because it was < 2 characters long 791s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '13' because it was < 2 characters long 791s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '16' because it was < 2 characters long 791s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '17' because it was < 2 characters long 791s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '22' because it was < 2 characters long 791s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '28' because it was < 2 characters long 791s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '29' because it was < 2 characters long 791s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '34' because it was < 2 characters long 791s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '43' because it was < 2 characters long 791s 44 reads; of these: 791s 44 (100.00%) were unpaired; of these: 791s 44 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s --- Summary --- 791s Read 1 reference strings 791s Checked 0 alignments, 0 edits 791s --------------- 791s PASSED 791s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 791s /usr/bin/bowtie2 --cp-ival 2 --n-ceil 0.180609625928019,0.203931122708202 --local --cp-min 10 --nofw --trim5 7 -M 2 --rdg 40.7969223543715,9.78865881079622 --score-min L,6.1556780539605,7.55898349662945 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 791s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 791s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '6' because it was < 2 characters long 791s Warning: skipping read '13' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '13' because it was < 2 characters long 791s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '16' because it was < 2 characters long 791s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '17' because it was < 2 characters long 791s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '22' because it was < 2 characters long 791s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '28' because it was < 2 characters long 791s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '29' because it was < 2 characters long 791s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '34' because it was < 2 characters long 791s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '43' because it was < 2 characters long 791s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 791s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 791s 44 reads; of these: 791s 44 (100.00%) were unpaired; of these: 791s 44 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s Flattened IUPAC characters 791s Mutating sequence Sim.pm.2 791s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 791s Introducing 12 SNPs, 0/1 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutating sequence Sim.pm.1 791s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutated reference genome to subject genome 791s SNPs introduced: 16 791s Reference gaps introduced: 0 791s Read gaps introduced: 1 791s Rearrangements introduced: 0 791s Created read sampler 791s Sampling 61 reads 791s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 791s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 791s parsing sequence Sim.pm.1... 791s parsing sequence Sim.pm.2... 791s Parsed 86 reference bases 791s *** Run 80 of 100 791s /usr/bin/bowtie2 --cp-min 2 --trim5 0 -i S,2.78291566602319 -M 2 --norc --trim3 5 --cp-ival 2 --nofw --mp 6.00992553208194,3.5783788446161 --mm --score-min L,6.86318107152842,5.19950415564601 --rdg 49.3209477599154,4.97403597402995 --rfg 22.6754462590501 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 791s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 791s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 791s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '7' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 791s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '8' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 791s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '16' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 791s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '22' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 791s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '23' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 791s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '27' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 791s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '35' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 791s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '36' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 791s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '37' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 791s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '42' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 791s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '45' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 791s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '49' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 791s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '51' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 791s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '53' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 791s 61 reads; of these: 791s 61 (100.00%) were unpaired; of these: 791s 61 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s Read 50 alignments... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s /usr/bin/bowtie2 --cp-min 2 --trim5 0 -i S,2.78291566602319 -M 2 --norc --trim3 5 --cp-ival 2 --nofw --mp 6.00992553208194,3.5783788446161 --mm --score-min L,6.86318107152842,5.19950415564601 --rdg 49.3209477599154,4.97403597402995 --rfg 22.6754462590501 -f -p 4 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s --- Summary --- 791s Read 1 reference strings 791s Checked 0 alignments, 0 edits 791s --------------- 791s PASSED 791s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 791s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 791s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 791s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '7' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 791s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '8' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 791s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '16' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 791s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '22' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 791s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '23' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 791s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '27' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 791s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '35' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 791s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '36' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 791s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '37' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 791s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '42' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 791s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '45' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 791s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '49' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 791s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '51' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 791s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '53' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 791s 61 reads; of these: 791s 61 (100.00%) were unpaired; of these: 791s 61 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 791s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 791s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 791s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 791s /usr/bin/bowtie2 --cp-min 2 --trim5 0 -i S,2.78291566602319 -M 2 --norc --trim3 5 --cp-ival 2 --nofw --mp 6.00992553208194,3.5783788446161 --mm --score-min L,6.86318107152842,5.19950415564601 --rdg 49.3209477599154,4.97403597402995 --rfg 22.6754462590501 -f -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 791s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 791s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 791s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '7' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 791s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '8' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 791s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '16' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 791s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '22' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 791s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '23' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 791s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '27' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 791s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '35' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 791s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '36' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 791s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '37' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 791s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 791s Warning: skipping read '42' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 791s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '45' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 791s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '49' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 791s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '51' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 791s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 791s Warning: skipping read '53' because it was < 2 characters long 791s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 791s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 791s 61 reads; of these: 791s 61 (100.00%) were unpaired; of these: 791s 61 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 791s Flattened IUPAC characters 791s Mutating sequence Sim.pm.2 791s Introducing 2 SNPs, 0/0 ref/read gaps, and 2 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutating sequence Sim.pm.1 791s Introducing 3 SNPs, 0/2 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutated reference genome to subject genome 791s SNPs introduced: 5 791s Reference gaps introduced: 0 791s Read gaps introduced: 2 791s Rearrangements introduced: 2 791s Created read sampler 791s Sampling 83 reads 791s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 791s *** Run 81 of 100 791s /usr/bin/bowtie2 --cp-ival 3 --local -N 1 -L17 --trim3 6 --rfg 41.2686349893147,19.5674787872637 --score-min L,8.95734841906215,4.16712224632753 -a --cp-min 2 -i C,0.535880283242941,10.9787810347957 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw 791s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 791s parsing sequence Sim.pm.1... 791s parsing sequence Sim.pm.2... 791s Parsed 86 reference bases 791s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '8' because it was < 2 characters long 791s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '11' because it was < 2 characters long 791s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '14' because it was < 2 characters long 791s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '18' because it was < 2 characters long 791s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '20' because it was < 2 characters long 791s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '21' because it was < 2 characters long 791s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '24' because it was < 2 characters long 791s Warning: skipping mate #2 of read '24' because it was < 2 characters long 791s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '38' because it was < 2 characters long 791s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '42' because it was < 2 characters long 791s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '43' because it was < 2 characters long 791s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '55' because it was < 2 characters long 791s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '60' because it was < 2 characters long 791s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '62' because it was < 2 characters long 791s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '67' because it was < 2 characters long 791s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '73' because it was < 2 characters long 791s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '77' because it was < 2 characters long 791s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '79' because it was < 2 characters long 791s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '80' because it was < 2 characters long 791s Warning: skipping mate #1 of read '81' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '81' because it was < 2 characters long 791s Read 50 alignments... 791s 83 reads; of these: 791s 68 (81.93%) were paired; of these: 791s 68 (100.00%) aligned concordantly 0 times 791s 0 (0.00%) aligned concordantly exactly 1 time 791s 0 (0.00%) aligned concordantly >1 times 791s ---- 791s 68 pairs aligned concordantly 0 times; of these: 791s 0 (0.00%) aligned discordantly 1 time 791s ---- 791s 68 pairs aligned 0 times concordantly or discordantly; of these: 791s 136 mates make up the pairs; of these: 791s 136 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 15 (18.07%) were unpaired; of these: 791s 15 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s Read 100 alignments... 791s Read 150 alignments... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s /usr/bin/bowtie2 --cp-ival 3 --local -N 1 -L17 --trim3 6 --rfg 41.2686349893147,19.5674787872637 --score-min L,8.95734841906215,4.16712224632753 -a --cp-min 2 -i C,0.535880283242941,10.9787810347957 -r -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s --- Summary --- 791s Read 1 reference strings 791s Checked 0 alignments, 0 edits 791s --------------- 791s PASSED 791s ALSO checking that bowtie2 and bowtie2-align match up 791s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 791s /usr/bin/bowtie2 --cp-ival 3 --local -N 1 -L17 --trim3 6 --rfg 41.2686349893147,19.5674787872637 --score-min L,8.95734841906215,4.16712224632753 -a --cp-min 2 -i C,0.535880283242941,10.9787810347957 -r -p 3 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 791s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '8' because it was < 2 characters long 791s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '11' because it was < 2 characters long 791s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '14' because it was < 2 characters long 791s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '18' because it was < 2 characters long 791s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '20' because it was < 2 characters long 791s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '21' because it was < 2 characters long 791s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '24' because it was < 2 characters long 791s Warning: skipping mate #2 of read '24' because it was < 2 characters long 791s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '38' because it was < 2 characters long 791s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '42' because it was < 2 characters long 791s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '43' because it was < 2 characters long 791s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '55' because it was < 2 characters long 791s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '60' because it was < 2 characters long 791s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '62' because it was < 2 characters long 791s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '67' because it was < 2 characters long 791s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '73' because it was < 2 characters long 791s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '77' because it was < 2 characters long 791s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '79' because it was < 2 characters long 791s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '80' because it was < 2 characters long 791s Warning: skipping mate #1 of read '81' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '81' because it was < 2 characters long 791s 83 reads; of these: 791s 68 (81.93%) were paired; of these: 791s 68 (100.00%) aligned concordantly 0 times 791s 0 (0.00%) aligned concordantly exactly 1 time 791s 0 (0.00%) aligned concordantly >1 times 791s ---- 791s 68 pairs aligned concordantly 0 times; of these: 791s 0 (0.00%) aligned discordantly 1 time 791s ---- 791s 68 pairs aligned 0 times concordantly or discordantly; of these: 791s 136 mates make up the pairs; of these: 791s 136 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 15 (18.07%) were unpaired; of these: 791s 15 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 791s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '8' because it was < 2 characters long 791s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '11' because it was < 2 characters long 791s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '14' because it was < 2 characters long 791s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '18' because it was < 2 characters long 791s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '20' because it was < 2 characters long 791s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '21' because it was < 2 characters long 791s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '24' because it was < 2 characters long 791s Warning: skipping mate #2 of read '24' because it was < 2 characters long 791s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '38' because it was < 2 characters long 791s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '42' because it was < 2 characters long 791s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '43' because it was < 2 characters long 791s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '55' because it was < 2 characters long 791s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '60' because it was < 2 characters long 791s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '62' because it was < 2 characters long 791s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '67' because it was < 2 characters long 791s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '73' because it was < 2 characters long 791s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '77' because it was < 2 characters long 791s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '79' because it was < 2 characters long 791s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '80' because it was < 2 characters long 791s Warning: skipping mate #1 of read '81' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '81' because it was < 2 characters long 791s 83 reads; of these: 791s 68 (81.93%) were paired; of these: 791s 68 (100.00%) aligned concordantly 0 times 791s 0 (0.00%) aligned concordantly exactly 1 time 791s 0 (0.00%) aligned concordantly >1 times 791s ---- 791s 68 pairs aligned concordantly 0 times; of these: 791s 0 (0.00%) aligned discordantly 1 time 791s ---- 791s 68 pairs aligned 0 times concordantly or discordantly; of these: 791s 136 mates make up the pairs; of these: 791s 136 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 15 (18.07%) were unpaired; of these: 791s 15 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 791s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 791s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 791s /usr/bin/bowtie2 --cp-ival 3 --local -N 1 -L17 --trim3 6 --rfg 41.2686349893147,19.5674787872637 --score-min L,8.95734841906215,4.16712224632753 -a --cp-min 2 -i C,0.535880283242941,10.9787810347957 -r -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.raw -2 /tmp/Sim.pm.GP7sSa1l_2.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 791s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 791s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '8' because it was < 2 characters long 791s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '11' because it was < 2 characters long 791s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '14' because it was < 2 characters long 791s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '18' because it was < 2 characters long 791s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '20' because it was < 2 characters long 791s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '21' because it was < 2 characters long 791s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '24' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '24' because it was < 2 characters long 791s Warning: skipping mate #2 of read '24' because it was < 2 characters long 791s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '38' because it was < 2 characters long 791s Warning: skipping mate #1 of read '42' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '42' because it was < 2 characters long 791s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '43' because it was < 2 characters long 791s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '55' because it was < 2 characters long 791s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '60' because it was < 2 characters long 791s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '62' because it was < 2 characters long 791s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '67' because it was < 2 characters long 791s Warning: skipping mate #2 of read '73' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #2 of read '73' because it was < 2 characters long 791s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '77' because it was < 2 characters long 791s Warning: skipping mate #1 of read '79' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '79' because it was < 2 characters long 791s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '80' because it was < 2 characters long 791s Warning: skipping mate #1 of read '81' because length (1) <= # seed mismatches (1) 791s Warning: skipping mate #1 of read '81' because it was < 2 characters long 791s 83 reads; of these: 791s 68 (81.93%) were paired; of these: 791s 68 (100.00%) aligned concordantly 0 times 791s 0 (0.00%) aligned concordantly exactly 1 time 791s 0 (0.00%) aligned concordantly >1 times 791s ---- 791s 68 pairs aligned concordantly 0 times; of these: 791s 0 (0.00%) aligned discordantly 1 time 791s ---- 791s 68 pairs aligned 0 times concordantly or discordantly; of these: 791s 136 mates make up the pairs; of these: 791s 136 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 15 (18.07%) were unpaired; of these: 791s 15 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 791s Flattened IUPAC characters 791s Mutating sequence Sim.pm.1 791s Introducing 1 SNPs, 0/2 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutating sequence Sim.pm.2 791s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutated reference genome to subject genome 791s SNPs introduced: 7 791s Reference gaps introduced: 0 791s Read gaps introduced: 3 791s Rearrangements introduced: 1 791s Created read sampler 791s Sampling 37 reads 791s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 791s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 791s parsing sequence Sim.pm.1... 791s parsing sequence Sim.pm.2... 791s Parsed 86 reference bases 791s *** Run 82 of 100 791s /usr/bin/bowtie2 --trim3 4 --cp-min 4 --cp-ival 2 --local --mm -M 2 --score-min L,8.47312324271327,4.23907487807859 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 791s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 791s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 791s Warning: skipping mate #1 of read '16' because it was < 2 characters long 791s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 791s Warning: skipping mate #2 of read '22' because it was < 2 characters long 791s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 791s Warning: skipping mate #2 of read '31' because it was < 2 characters long 791s 37 reads; of these: 791s 32 (86.49%) were paired; of these: 791s 32 (100.00%) aligned concordantly 0 times 791s 0 (0.00%) aligned concordantly exactly 1 time 791s 0 (0.00%) aligned concordantly >1 times 791s ---- 791s 32 pairs aligned concordantly 0 times; of these: 791s 0 (0.00%) aligned discordantly 1 time 791s ---- 791s 32 pairs aligned 0 times concordantly or discordantly; of these: 791s 64 mates make up the pairs; of these: 791s 64 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 5 (13.51%) were unpaired; of these: 791s 5 (100.00%) aligned 0 times 791s 0 (0.00%) aligned exactly 1 time 791s 0 (0.00%) aligned >1 times 791s 0.00% overall alignment rate 791s Read 50 alignments... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s Processing line... 791s --- Summary --- 791s Read 1 reference strings 791s Checked 0 alignments, 0 edits 791s --------------- 791s PASSED 791s Flattened IUPAC characters 791s Mutating sequence Sim.pm.2 791s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutating sequence Sim.pm.1 791s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 791s Finished SNPs 791s Finished ref gaps 791s Finished read gaps 791s Mutated reference genome to subject genome 791s SNPs introduced: 1 791s Reference gaps introduced: 0 791s Read gaps introduced: 1 791s Rearrangements introduced: 0 791s Created read sampler 791s Sampling 110 reads 791s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 791s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 791s parsing sequence Sim.pm.1... 791s parsing sequence Sim.pm.2... 791s Parsed 86 reference bases 791s *** Run 83 of 100 791s /usr/bin/bowtie2 --local --cp-ival 2 -D 6 --trim3 3 --rdg 5.04376506652684 --score-min L,1.56822185325383,1.63865597326577 --cp-min 3 -R 2 -k 3 --trim5 3 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 792s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '8' because it was < 2 characters long 792s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '9' because it was < 2 characters long 792s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '16' because it was < 2 characters long 792s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '19' because it was < 2 characters long 792s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '25' because it was < 2 characters long 792s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '27' because it was < 2 characters long 792s Warning: skipping read '32' because length (1) <= # seed mismatches (0) 792s Warning: skipping read '32' because it was < 2 characters long 792s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '34' because it was < 2 characters long 792s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '38' because it was < 2 characters long 792s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '47' because it was < 2 characters long 792s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '57' because it was < 2 characters long 792s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '63' because it was < 2 characters long 792s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '64' because it was < 2 characters long 792s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '70' because it was < 2 characters long 792s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '77' because it was < 2 characters long 792s Warning: skipping read '96' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '96' because it was < 2 characters long 792s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '101' because it was < 2 characters long 792s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '104' because it was < 2 characters long 792s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '105' because it was < 2 characters long 792s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '109' because it was < 2 characters long 792s 110 reads; of these: 792s 110 (100.00%) were unpaired; of these: 792s 74 (67.27%) aligned 0 times 792s 27 (24.55%) aligned exactly 1 time 792s 9 (8.18%) aligned >1 times 792s 32.73% overall alignment rate 792s Read 50 alignments... 792s Read 100 alignments... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CCG 792s CCG 792s Processing line... 792s CCG 792s CCG 792s Processing line... 792s CCG 792s CCG 792s Processing line... 792s ATCTCAAAT 792s ATCTCAAAT 792s Processing line... 792s TGT 792s TGT 792s Processing line... 792s Processing line... 792s GCA 792s GCA 792s Processing line... 792s GCA 792s GCA 792s Processing line... 792s TGC 792s TGC 792s Processing line... 792s Processing line... 792s ATGACTGG 792s ATGACTGG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GTGCAATTCGAATCATGACTGGATCTCAAATAAAAGGGCCAC 792s GTGCAATTCGAATCATGACTGGATCTCAAATNAAAGGGCCAC 792s Processing line... 792s GTGCAATTCG 792s GTGCAATTCG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TCA 792s TCA 792s Processing line... 792s TCA 792s TCA 792s Processing line... 792s TGA 792s TGA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GTGCAATTCGAATCATGACTGGATCTCAAATGAAA 792s GTGCAATTCGAATCATGACTGGATCTCAAATNAAA 792s Processing line... 792s GG 792s GG 792s Processing line... 792s GG 792s GG 792s Processing line... 792s GG 792s GG 792s Processing line... 792s GAA 792s GAA 792s Processing line... 792s TTC 792s TTC 792s Processing line... 792s TTC 792s TTC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s ACGGC 792s ACGGC 792s Processing line... 792s Processing line... 792s Processing line... 792s CGAATCATG 792s CGAATCATG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CCACCGGGAGG 792s CCACCGGGAGG 792s Processing line... 792s Processing line... 792s GGAT 792s GGAT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TC 792s TC 792s Processing line... 792s TC 792s TC 792s Processing line... 792s TC 792s TC 792s Processing line... 792s TGT 792s TGT 792s Processing line... 792s GTGCAATTCGAATCATGACTGGATCTCAAATAAAAGG 792s GTGCAATTCGAATCATGACTGGATCTCAAATNAAAGG 792s Processing line... 792s ATCT 792s ATCT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s GT 792s GT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CATGACTGGATCTCAAATAAAAGGGC 792s CATGACTGGATCTCAAATNAAAGGGC 792s Processing line... 792s TCTTT 792s TCTTT 792s Processing line... 792s TGCAATTCGAATCATGACTGGATCTCAAAT 792s TGCAATTCGAATCATGACTGGATCTCAAAT 792s Processing line... 792s Processing line... 792s Processing line... 792s ACTGGATCTC 792s ACTGGATCTC 792s Processing line... 792s Processing line... 792s TTT 792s TTT 792s Processing line... 792s AAA 792s AAA 792s Processing line... 792s AAA 792s AAA 792s Processing line... 792s TGTGCAATTCGAATCATGACTGGATCTCAAATGAAAGGGCCACC-GGA 792s TGTGCAATTCGAATCATGACTGGATCTCAAATNAAAGGGCCACCGGGA 792s Processing line... 792s CCCTCTTTC 792s CCCTCTTTC 792s Processing line... 792s TGGAT 792s TGGAT 792s Processing line... 792s Processing line... 792s GCCA 792s GCCA 792s Processing line... 792s GCCA 792s GCCA 792s Processing line... 792s Processing line... 792s Processing line... 792s CGAATCATGACTGGATCTCA 792s CGAATCATGACTGGATCTCA 792s Processing line... 792s CGCCACCC 792s CGCCACCC 792s Processing line... 792s AACGGC 792s AACGGC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CCAACGGCCGCCACCCTCTTTCCCGC 792s CCAACGGCCGCCACCCTCTTTCCCGC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TTCGAATCATGACT 792s TTCGAATCATGACT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TTCGAATCATG 792s TTCGAATCATG 792s Processing line... 792s Processing line... 792s CATGACT 792s CATGACT 792s Processing line... 792s --- Summary --- 792s Read 1 reference strings 792s Checked 53 alignments, 0 edits 792s --------------- 792s PASSED 792s Flattened IUPAC characters 792s Mutating sequence Sim.pm.1 792s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutating sequence Sim.pm.2 792s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutated reference genome to subject genome 792s SNPs introduced: 4 792s Reference gaps introduced: 1 792s Read gaps introduced: 0 792s Rearrangements introduced: 2 792s Created read sampler 792s Sampling 53 reads 792s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 792s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 792s parsing sequence Sim.pm.1... 792s *** Run 84 of 100 792s /usr/bin/bowtie2 --cp-ival 1 --mp 5.64419190574266,4.01885237060602 --trim3 5 --gbar 4 --score-min L,3.17547230185715,6.88038963909872 -a --cp-min 2 --np 2 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 792s parsing sequence Sim.pm.2... 792s Parsed 86 reference bases 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 792s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '22' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 792s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '30' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 792s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '52' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 792s 53 reads; of these: 792s 45 (84.91%) were paired; of these: 792s 45 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 45 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 45 pairs aligned 0 times concordantly or discordantly; of these: 792s 90 mates make up the pairs; of these: 792s 76 (84.44%) aligned 0 times 792s 10 (11.11%) aligned exactly 1 time 792s 4 (4.44%) aligned >1 times 792s 8 (15.09%) were unpaired; of these: 792s 7 (87.50%) aligned 0 times 792s 1 (12.50%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 15.31% overall alignment rate 792s Read 50 alignments... 792s Read 100 alignments... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s ATT 792s ATT 792s Processing line... 792s AAT 792s AAT 792s Processing line... 792s AAT 792s AAT 792s Processing line... 792s AAT 792s AAT 792s Processing line... 792s AAT 792s AAT 792s Processing line... 792s Processing line... 792s ACTGGATCTCA 792s ACTGGATCTCA 792s Processing line... 792s Processing line... 792s TGGATCTCA 792s TGGATCTCA 792s Processing line... 792s Processing line... 792s CGCCACCCTCTTTCCCG 792s CGCCACCCTCTTTCCCG 792s Processing line... 792s CCCG 792s CCCG 792s Processing line... 792s CGGG 792s CGGG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s ATTCG 792s ATTCG 792s Processing line... 792s CGAAT 792s CGAAT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GCAATTCGAATCATGACTGG 792s GCAATTCGAATCATGACTGG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TGACTGGAT 792s TGACTGGAT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CGAATCATG 792s CGAATCATG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CGAAT 792s CGAAT 792s Processing line... 792s ATTCG 792s ATTCG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AGGGC 792s AGGGC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TGCAATTCGAATCATGACT 792s TGCAATTCGAATCATGACT 792s Processing line... 792s Processing line... 792s CACCGGGAGG 792s CACCGGGAGG 792s Processing line... 792s Processing line... 792s CAATTCGAA 792s CAATTCGAA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CGAATCATG 792s CGAATCATG 792s Processing line... 792s Processing line... 792s Processing line... 792s --- Summary --- 792s Read 1 reference strings 792s Checked 22 alignments, 0 edits 792s --------------- 792s PASSED 792s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 792s /usr/bin/bowtie2 --cp-ival 1 --mp 5.64419190574266,4.01885237060602 --trim3 5 --gbar 4 --score-min L,3.17547230185715,6.88038963909872 -a --cp-min 2 --np 2 -f -p 2 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 792s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '22' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 792s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '30' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 792s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '52' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 792s 53 reads; of these: 792s 45 (84.91%) were paired; of these: 792s 45 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 45 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 45 pairs aligned 0 times concordantly or discordantly; of these: 792s 90 mates make up the pairs; of these: 792s 76 (84.44%) aligned 0 times 792s 10 (11.11%) aligned exactly 1 time 792s 4 (4.44%) aligned >1 times 792s 8 (15.09%) were unpaired; of these: 792s 7 (87.50%) aligned 0 times 792s 1 (12.50%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 15.31% overall alignment rate 792s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 792s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 792s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 792s Flattened IUPAC characters 792s Mutating sequence Sim.pm.2 792s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutating sequence Sim.pm.1 792s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutated reference genome to subject genome 792s SNPs introduced: 3 792s Reference gaps introduced: 1 792s Read gaps introduced: 0 792s Rearrangements introduced: 2 792s Created read sampler 792s Sampling 15 reads 792s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 792s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 792s parsing sequence Sim.pm.1... 792s parsing sequence Sim.pm.2... 792s Parsed 86 reference bases 792s *** Run 85 of 100 792s /usr/bin/bowtie2 --cp-min 16 --np 1 --trim3 5 --mp 7.49230146028363,2.25444226648081 --nofw --cp-ival 1 --local --rfg 21.5339533045823 --rdg 35.707469364691 --score-min L,7.55156644661126,5.00231697140119 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 792s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '7' because it was < 2 characters long 792s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '13' because it was < 2 characters long 792s 15 reads; of these: 792s 11 (73.33%) were paired; of these: 792s 11 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 11 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 11 pairs aligned 0 times concordantly or discordantly; of these: 792s 22 mates make up the pairs; of these: 792s 22 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 4 (26.67%) were unpaired; of these: 792s 4 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 0.00% overall alignment rate 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s --- Summary --- 792s Read 1 reference strings 792s Checked 0 alignments, 0 edits 792s --------------- 792s PASSED 792s Flattened IUPAC characters 792s Mutating sequence Sim.pm.1 792s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutating sequence Sim.pm.2 792s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutated reference genome to subject genome 792s SNPs introduced: 9 792s Reference gaps introduced: 0 792s Read gaps introduced: 1 792s Rearrangements introduced: 1 792s Created read sampler 792s Sampling 114 reads 792s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 792s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 792s *** Run 86 of 100 792s /usr/bin/bowtie2 -k 5 -i S,0.944082489817875,5.59827384578682 --np 7 --norc --cp-min 2 --gbar 3 --score-min L,2.00197971433786,9.9432893903831 --rfg 24.9772151126821,7.86819596206614 --cp-ival 2 --n-ceil 0.393944474628791,1.105358301874 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 792s parsing sequence Sim.pm.1... 792s parsing sequence Sim.pm.2... 792s Parsed 86 reference bases 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 792s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '13' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 792s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '16' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 792s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '17' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 792s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '24' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 792s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '28' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 792s Read 50 alignments... 792s Read 100 alignments... 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 792s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '83' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 792s Read 150 alignments... 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 792s Read 200 alignments... 792s 114 reads; of these: 792s 114 (100.00%) were paired; of these: 792s 114 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 114 pairs aligned concordantly 0 times; of these: 792s 1 (0.88%) aligned discordantly 1 time 792s ---- 792s 113 pairs aligned 0 times concordantly or discordantly; of these: 792s 226 mates make up the pairs; of these: 792s 207 (91.59%) aligned 0 times 792s 11 (4.87%) aligned exactly 1 time 792s 8 (3.54%) aligned >1 times 792s 9.21% overall alignment rate 792s Read 250 alignments... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AATCATGA 792s AATCATGA 792s Processing line... 792s Processing line... 792s CCG 792s CCG 792s Processing line... 792s CCG 792s CCG 792s Processing line... 792s CCG 792s CCG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CC 792s CC 792s Processing line... 792s CC 792s CC 792s Processing line... 792s CC 792s CC 792s Processing line... 792s CC 792s CC 792s Processing line... 792s /usr/bin/bowtie2 -k 5 -i S,0.944082489817875,5.59827384578682 --np 7 --norc --cp-min 2 --gbar 3 --score-min L,2.00197971433786,9.9432893903831 --rfg 24.9772151126821,7.86819596206614 --cp-ival 2 --n-ceil 0.393944474628791,1.105358301874 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 792s CC 792s CC 792s Processing line... 792s Processing line... 792s ACCGGG 792s ACCGGG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TCGAATCATGACTGGA 792s TCGAATCATGACTGGA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AACGGCCGCCACCCTCTTTCCCG 792s AACGGCCGCCACCCTCTTTCCCG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CCACC 792s CCACC 792s Processing line... 792s CCACC 792s CCACC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GTGCAATTCGAATCATGA 792s GTGCAATTCGAATCATGA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CC 792s CC 792s Processing line... 792s CC 792s CC 792s Processing line... 792s CC 792s CC 792s Processing line... 792s CC 792s CC 792s Processing line... 792s CC 792s CC 792s Processing line... 792s Processing line... 792s ATT 792s ATT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CGAATCAT 792s CGAATCAT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TTCGAATCAT 792s TTCGAATCAT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GA 792s GA 792s Processing line... 792s GA 792s GA 792s Processing line... 792s GA 792s GA 792s Processing line... 792s GA 792s GA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GAGGCAC 792s GAGGCAC 792s Processing line... 792s TGTGCAA 792s TGTGCAA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AA 792s AA 792s Processing line... 792s AA 792s AA 792s Processing line... 792s AA 792s AA 792s Processing line... 792s AA 792s AA 792s Processing line... 792s AA 792s AA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AGGGCCA 792s AGGGCCA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CGA 792s CGA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AAAGGGCCACCGGGAGG 792s AAAGGGCCACCGGGAGG 792s Processing line... 792s --- Summary --- 792s Read 1 reference strings 792s Checked 47 alignments, 0 edits 792s --------------- 792s PASSED 792s ALSO checking that bowtie2 and bowtie2-align match up 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 792s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '13' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 792s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '16' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 792s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '17' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 792s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '24' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 792s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '28' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 792s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 792s /usr/bin/bowtie2 -k 5 -i S,0.944082489817875,5.59827384578682 --np 7 --norc --cp-min 2 --gbar 3 --score-min L,2.00197971433786,9.9432893903831 --rfg 24.9772151126821,7.86819596206614 --cp-ival 2 --n-ceil 0.393944474628791,1.105358301874 -f -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 792s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '83' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 792s 114 reads; of these: 792s 114 (100.00%) were paired; of these: 792s 114 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 114 pairs aligned concordantly 0 times; of these: 792s 1 (0.88%) aligned discordantly 1 time 792s ---- 792s 113 pairs aligned 0 times concordantly or discordantly; of these: 792s 226 mates make up the pairs; of these: 792s 207 (91.59%) aligned 0 times 792s 11 (4.87%) aligned exactly 1 time 792s 8 (3.54%) aligned >1 times 792s 9.21% overall alignment rate 792s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 792s Warning: skipping mate #2 of read '13' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '13' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 792s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '16' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 792s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '17' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 792s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '24' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 792s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '28' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; settindiff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 792s *** Run 87 of 100 792s /usr/bin/bowtie2 --cp-ival 1 -N 0 -L12 --mp 8.33302814108664,3.65526957004234 --trim3 2 --gbar 2 --rfg 1.85757049773517 --score-min L,9.51725850858119,4.40291265176962 -a --cp-min 3 --ma 6.10619069357692 --trim5 4 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta 792s g to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 792s Warning: skipping mate #2 of read '83' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '83' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 792s 114 reads; of these: 792s 114 (100.00%) were paired; of these: 792s 114 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 114 pairs aligned concordantly 0 times; of these: 792s 1 (0.88%) aligned discordantly 1 time 792s ---- 792s 113 pairs aligned 0 times concordantly or discordantly; of these: 792s 226 mates make up the pairs; of these: 792s 207 (91.59%) aligned 0 times 792s 11 (4.87%) aligned exactly 1 time 792s 8 (3.54%) aligned >1 times 792s 9.21% overall alignment rate 792s Flattened IUPAC characters 792s Mutating sequence Sim.pm.1 792s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutating sequence Sim.pm.2 792s Introducing 4 SNPs, 1/2 ref/read gaps, and 0 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutated reference genome to subject genome 792s SNPs introduced: 6 792s Reference gaps introduced: 1 792s Read gaps introduced: 2 792s Rearrangements introduced: 0 792s Created read sampler 792s Sampling 57 reads 792s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 792s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 792s parsing sequence Sim.pm.1... 792s parsing sequence Sim.pm.2... 792s Parsed 86 reference bases 792s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 792s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '7' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 792s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '12' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 792s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '24' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 792s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '31' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 792s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '34' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 792s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '37' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 792s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '44' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 792s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '46' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 792s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '51' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 792s 57 reads; of these: 792s 51 (89.47%) were paired; of these: 792s 51 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 51 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 51 pairs aligned 0 times concordantly or discordantly; of these: 792s 102 mates make up the pairs; of these: 792s 90 (88.24%) aligned 0 times 792s 8 (7.84%) aligned exactly 1 time 792s 4 (3.92%) aligned >1 times 792s 6 (10.53%) were unpaired; of these: 792s 6 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 11.11% overall alignment rate 792s Read 50 alignments... 792s Read 100 alignments... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GGGA 792s GGGA 792s Processing line... 792s TCCC 792s TCCC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CCAAC 792s CCAAC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AATC 792s AATC 792s Processing line... 792s AATC 792s AATC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CCGGGAGG 792s CCGGGAGG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TGAC 792s TGAC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AGGGC 792s AGGGC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TC 792s TC 792s Processing line... 792s GA 792s GA 792s Processing line... 792s GA 792s GA 792s Processing line... 792s TC 792s TC 792s Processing line... 792s TC 792s TC 792s Processing line... 792s GA 792s GA 792s Processing line... 792s TC 792s TC 792s Processing line... 792s GA 792s GA 792s Processing line... 792s TC 792s TC 792s Processing line... 792s TC 792s TC 792s Processing line... 792s TC 792s TC 792s Processing line... 792s Processing line... 792s ACCGG 792s ACCGG 792s Processing line... 792s Processing line... 792s ACCGG 792s ACCGG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GT 792s GT 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s AC 792s AC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GGGCC 792s GGGCC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CACCG 792s CACCG 792s Processing line... 792s --- Summary --- 792s Read 1 reference strings 792s Checked 29 alignments, 0 edits 792s --------------- 792s PASSED 792s ALSO checking that bowtie2 and bowtie2-align match up 792s /usr/bin/bowtie2 --cp-ival 1 -N 0 -L12 --mp 8.33302814108664,3.65526957004234 --trim3 2 --gbar 2 --rfg 1.85757049773517 --score-min L,9.51725850858119,4.40291265176962 -a --cp-min 3 --ma 6.10619069357692 --trim5 4 -f -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 792s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 792s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '7' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 792s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '12' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 792s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '24' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 792s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '31' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 792s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '34' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 792s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '37' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 792s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '44' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 792s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '46' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 792s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '51' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 792s 57 reads; of these: 792s 51 (89.47%) were paired; of these: 792s 51 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 51 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 51 pairs aligned 0 times concordantly or discordantly; of these: 792s 102 mates make up the pairs; of these: 792s 90 (88.24%) aligned 0 times 792s 8 (7.84%) aligned exactly 1 time 792s 4 (3.92%) aligned >1 times 792s 6 (10.53%) were unpaired; of these: 792s 6 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 11.11% overall alignment rate 792s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 792s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 792s /usr/bin/bowtie2 --cp-ival 1 -N 0 -L12 --mp 8.33302814108664,3.65526957004234 --trim3 2 --gbar 2 --rfg 1.85757049773517 --score-min L,9.51725850858119,4.40291265176962 -a --cp-min 3 --ma 6.10619069357692 --trim5 4 -f -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.fasta -2 /tmp/Sim.pm.GP7sSa1l_2.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 792s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 792s Warning: skipping mate #1 of read '7' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '7' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 792s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '12' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 792s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '24' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 792s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '31' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 792s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '34' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 792s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '37' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 792s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '44' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 792s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '46' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 792s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '51' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 792s 57 reads; of these: 792s 51 (89.47%) were paired; of these: 792s 51 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 51 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 51 pairs aligned 0 times concordantly or discordantly; of these: 792s 102 mates make up the pairs; of these: 792s 90 (88.24%) aligned 0 times 792s 8 (7.84%) aligned exactly 1 time 792s 4 (3.92%) aligned >1 times 792s 6 (10.53%) were unpaired; of these: 792s 6 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 11.11% overall alignment rate 792s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 792s Flattened IUPAC characters 792s Mutating sequence Sim.pm.1 792s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutating sequence Sim.pm.2 792s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutated reference genome to subject genome 792s SNPs introduced: 2 792s Reference gaps introduced: 0 792s Read gaps introduced: 2 792s Rearrangements introduced: 1 792s Created read sampler 792s Sampling 103 reads 792s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 792s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 792s parsing sequence Sim.pm.1... 792s parsing sequence Sim.pm.2... 792s Parsed 86 reference bases 792s *** Run 88 of 100 792s /usr/bin/bowtie2 --cp-min 7 --n-ceil 1.02163241074363,0.251849357926843 --cp-ival 1 --mp 4.03624337868797,3.80756987987246 --np 2 --score-min L,8.512151527001,2.06299102835089 --rdg 37.3313858542441 --trim5 2 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 792s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 792s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '14' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 792s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '16' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 792s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '17' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 792s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '19' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 792s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '29' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 792s Warning: skipping read '30' because length (1) <= # seed mismatches (0) 792s Warning: skipping read '30' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 792s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '59' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 792s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '63' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 792s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 792s Warning: skipping read '70' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 792s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '73' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 792s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '75' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 792s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '78' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 792s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '80' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 792s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '92' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 792s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '94' because it was < 2 characters long 792s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 792s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 792s 103 reads; of these: 792s 103 (100.00%) were unpaired; of these: 792s 75 (72.82%) aligned 0 times 792s 21 (20.39%) aligned exactly 1 time 792s 7 (6.80%) aligned >1 times 792s 27.18% overall alignment rate 792s Read 50 alignments... 792s Read 100 alignments... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TGCAATTCGAATCATGACTG 792s TGCAATTCGAATCATGACTG 792s Processing line... 792s Processing line... 792s Processing line... 792s CACCGGGAGGCA 792s CACCGGGAGGCA 792s Processing line... 792s Processing line... 792s CGAATCATGACTG 792s CGAATCATGACTG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AGGCAC 792s AGGCAC 792s Processing line... 792s Processing line... 792s ACT 792s ACT 792s Processing line... 792s Processing line... 792s Processing line... 792s CAATTCGAATCATG 792s CAATTCGAATCATG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AAGGGCCACCG 792s AAGGGCCACCG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GGCCGCCACCC 792s GGCCGCCACCC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s TCGAATCAT 792s TCGAATCAT 792s Processing line... 792s CACCCTCTT 792s CACCCTCTT 792s Processing line... 792s ATCATGACTGGATCTCAA 792s ATCATGACTGGATCTCAA 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AAG 792s AAG 792s Processing line... 792s CCTCTTTCCC 792s CCTCTTTCCC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s CATGACTG 792s CATGACTG 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GGC 792s GGC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s AC 792s AC 792s Processing line... 792s TCGAATCATGACT 792s TCGAATCATGACT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s GGCCGCCACC 792s GGCCGCCACC 792s Processing line... 792s Processing line... 792s CCTCTTT 792s CCTCTTT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s ATCATGACTGGA 792s ATCATGACTGGA 792s Processing line... 792s Processing line... 792s CCACCCTCTTTC 792s CCACCCTCTTTC 792s Processing line... 792s Processing line... 792s Processing line... 792s CA 792s CA 792s Processing line... 792s Processing line... 792s TGCA 792s TGCA 792s Processing line... 792s AATTCGAATCATGACT 792s AATTCGAATCATGACT 792s Processing line... 792s AT 792s AT 792s Processing line... 792s Processing line... 792s Processing line... 792s CCGC 792s CCGC 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s ACTGGATCTCAAA 792s ACTGGATCTCAAA 792s Processing line... 792s Processing line... 792s CACCCT 792s CACCCT 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s --- Summary --- 792s Read 1 reference strings 792s Checked 28 alignments, 0 edits 792s --------------- 792s PASSED 792s Flattened IUPAC characters 792s Mutating sequence Sim.pm.1 792s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutating sequence Sim.pm.2 792s Introducing 6 SNPs, 0/0 ref/read gaps, and 1 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutated reference genome to subject genome 792s SNPs introduced: 11 792s Reference gaps introduced: 1 792s Read gaps introduced: 0 792s Rearrangements introduced: 1 792s Created read sampler 792s Sampling 114 reads 792s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 792s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 792s parsing sequence Sim.pm.1... 792s parsing sequence Sim.pm.2... 792s Parsed 86 reference bases 792s *** Run 89 of 100 792s /usr/bin/bowtie2 --mm -a --score-min L,1.75645690052716,6.32389236312865 --rfg 34.2477930509776 --rdg 45.246842687941 --trim3 9 --mp 8.7678720537895,5.65584172902002 --n-ceil 0.537675999432085,1.48443089713185 --cp-ival 1 --local --cp-min 8 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 792s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '10' because it was < 2 characters long 792s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '11' because it was < 2 characters long 792s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '19' because it was < 2 characters long 792s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '22' because it was < 2 characters long 792s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '24' because it was < 2 characters long 792s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '28' because it was < 2 characters long 792s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '29' because it was < 2 characters long 792s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '37' because it was < 2 characters long 792s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '39' because it was < 2 characters long 792s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '41' because it was < 2 characters long 792s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '43' because it was < 2 characters long 792s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '44' because it was < 2 characters long 792s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '46' because it was < 2 characters long 792s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '48' because it was < 2 characters long 792s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '51' because it was < 2 characters long 792s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '55' because it was < 2 characters long 792s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '57' because it was < 2 characters long 792s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '66' because it was < 2 characters long 792s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '69' because it was < 2 characters long 792s Warning: skipping mate #2 of read '74' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '74' because it was < 2 characters long 792s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '76' because it was < 2 characters long 792s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '77' because it was < 2 characters long 792s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '78' because it was < 2 characters long 792s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '82' because it was < 2 characters long 792s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '86' because it was < 2 characters long 792s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 792s Warning: skipping read '92' because it was < 2 characters long 792s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '96' because it was < 2 characters long 792s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '97' because it was < 2 characters long 792s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '98' because it was < 2 characters long 792s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '100' because it was < 2 characters long 792s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '103' because it was < 2 characters long 792s Warning: skipping mate #1 of read '107' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '107' because it was < 2 characters long 792s Read 50 alignments... 792s 114 reads; of these: 792s 89 (78.07%) were paired; of these: 792s 89 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 89 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 89 pairs aligned 0 times concordantly or discordantly; of these: 792s 178 mates make up the pairs; of these: 792s 178 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 25 (21.93%) were unpaired; of these: 792s 25 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 0.00% overall alignment rate 792s Read 100 alignments... 792s Read 150 alignments... 792s Read 200 alignments... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing 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Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s --- Summary --- 792s Read 1 reference strings 792s Checked 0 alignments, 0 edits 792s --------------- 792s PASSED 792s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 792s /usr/bin/bowtie2 --mm -a --score-min L,1.75645690052716,6.32389236312865 --rfg 34.2477930509776 --rdg 45.246842687941 --trim3 9 --mp 8.7678720537895,5.65584172902002 --n-ceil 0.537675999432085,1.48443089713185 --cp-ival 1 --local --cp-min 8 -q -p 2 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 792s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '10' because it was < 2 characters long 792s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '11' because it was < 2 characters long 792s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '19' because it was < 2 characters long 792s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '22' because it was < 2 characters long 792s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '24' because it was < 2 characters long 792s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '28' because it was < 2 characters long 792s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '29' because it was < 2 characters long 792s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '37' because it was < 2 characters long 792s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '39' because it was < 2 characters long 792s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '41' because it was < 2 characters long 792s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '43' because it was < 2 characters long 792s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '44' because it was < 2 characters long 792s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '46' because it was < 2 characters long 792s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '48' because it was < 2 characters long 792s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '51' because it was < 2 characters long 792s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '55' because it was < 2 characters long 792s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '57' because it was < 2 characters long 792s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '66' because it was < 2 characters long 792s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '69' because it was < 2 characters long 792s Warning: skipping mate #2 of read '74' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '74' because it was < 2 characters long 792s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '76' because it was < 2 characters long 792s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '77' because it was < 2 characters long 792s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '78' because it was < 2 characters long 792s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '82' because it was < 2 characters long 792s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '86' because it was < 2 characters long 792s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 792s Warning: skipping read '92' because it was < 2 characters long 792s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '96' because it was < 2 characters long 792s Warning: skipping mate #2 of read '97' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #2 of read '97' because it was < 2 characters long 792s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '98' because it was < 2 characters long 792s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '100' because it was < 2 characters long 792s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 792s Warning: skipping read '103' because it was < 2 characters long 792s Warning: skipping mate #1 of read '107' because length (1) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '107' because it was < 2 characters long 792s 114 reads; of these: 792s 89 (78.07%) were paired; of these: 792s 89 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 89 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 89 pairs aligned 0 times concordantly or discordantly; of these: 792s 178 mates make up the pairs; of these: 792s 178 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 25 (21.93%) were unpaired; of these: 792s 25 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 0.00% overall alignment rate 792s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 792s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 792s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 792s Flattened IUPAC characters 792s Mutating sequence Sim.pm.2 792s Introducing 10 SNPs, 0/0 ref/read gaps, and 1 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutating sequence Sim.pm.1 792s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 792s Finished SNPs 792s Finished ref gaps 792s Finished read gaps 792s Mutated reference genome to subject genome 792s SNPs introduced: 10 792s Reference gaps introduced: 0 792s Read gaps introduced: 1 792s Rearrangements introduced: 1 792s Created read sampler 792s Sampling 83 reads 792s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 792s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 792s parsing sequence Sim.pm.1... 792s parsing sequence Sim.pm.2... 792s Parsed 86 reference bases 792s *** Run 90 of 100 792s /usr/bin/bowtie2 --trim5 1 --np 1 --cp-min 6 --gbar 2 --rfg 26.7069600453096,19.854212339785 --rdg 7.6076088723013,18.9757438585806 --score-min L,8.45435668044739,1.07141532239984 --local --cp-ival 2 --nofw -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 792s Warning: skipping mate #1 of read '35' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '35' because it was < 2 characters long 792s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 792s Warning: skipping mate #1 of read '51' because it was < 2 characters long 792s Read 50 alignments... 792s 83 reads; of these: 792s 81 (97.59%) were paired; of these: 792s 81 (100.00%) aligned concordantly 0 times 792s 0 (0.00%) aligned concordantly exactly 1 time 792s 0 (0.00%) aligned concordantly >1 times 792s ---- 792s 81 pairs aligned concordantly 0 times; of these: 792s 0 (0.00%) aligned discordantly 1 time 792s ---- 792s 81 pairs aligned 0 times concordantly or discordantly; of these: 792s 162 mates make up the pairs; of these: 792s 160 (98.77%) aligned 0 times 792s 2 (1.23%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 2 (2.41%) were unpaired; of these: 792s 2 (100.00%) aligned 0 times 792s 0 (0.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 1.22% overall alignment rate 792s Read 100 alignments... 792s Read 150 alignments... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 792s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s AAGGGCCACCGGGAGGCA 793s AAGGGCCACCGGGAGGCA 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s GCCACCGGGAGGC 793s GCCACCGGGAGGC 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s --- Summary --- 793s Read 1 reference strings 793s Checked 2 alignments, 0 edits 793s --------------- 793s PASSED 793s Flattened IUPAC characters 793s Mutating sequence Sim.pm.2 793s Introducing 8 SNPs, 0/1 ref/read gaps, and 1 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutating sequence Sim.pm.1 793s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutated reference genome to subject genome 793s SNPs introduced: 9 793s Reference gaps introduced: 0 793s Read gaps introduced: 1 793s Rearrangements introduced: 1 793s Created read sampler 793s Sampling 123 reads 793s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 793s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 793s parsing sequence Sim.pm.1... 793s parsing sequence Sim.pm.2... 793s Parsed 86 reference bases 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s *** Run 91 of 100 793s /usr/bin/bowtie2 --mp 7.4095732377906,2.5847847721105 --ma 3.03534389194298 --cp-ival 1 --cp-min 13 --rfg 6.00209318156257,12.4705618969154 --rdg 41.9864492983782 --score-min L,4.34740533983775,7.90672918924689 --gbar 5 --np 3 --trim5 6 --mm -k 7 --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 793s 123 reads; of these: 793s 123 (100.00%) were unpaired; of these: 793s 109 (88.62%) aligned 0 times 793s 6 (4.88%) aligned exactly 1 time 793s 8 (6.50%) aligned >1 times 793s 11.38% overall alignment rate 793s Read 50 alignments... 793s Read 100 alignments... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s GGA 793s GGA 793s Processing line... 793s TCC 793s TCC 793s Processing line... 793s GGA 793s GGA 793s Processing line... 793s Processing line... 793s Processing line... 793s TGTG 793s TGTG 793s Processing line... 793s TCC 793s TCC 793s Processing line... 793s GGA 793s GGA 793s Processing line... 793s GGA 793s GGA 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s GCA 793s GCA 793s Processing line... 793s GCA 793s GCA 793s Processing line... 793s TGC 793s TGC 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s /usr/bin/bowtie2 --mp 7.4095732377906,2.5847847721105 --ma 3.03534389194298 --cp-ival 1 --cp-min 13 --rfg 6.00209318156257,12.4705618969154 --rdg 41.9864492983782 --score-min L,4.34740533983775,7.90672918924689 --gbar 5 --np 3 --trim5 6 --mm -k 7 --qseq -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 793s GGA 793s GGA 793s Processing line... 793s TCC 793s TCC 793s Processing line... 793s GGA 793s GGA 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s GGA 793s GGA 793s Processing line... 793s GGA 793s GGA 793s Processing line... 793s TCC 793s TCC 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s AAG 793s AAG 793s Processing line... 793s CTT 793s CTT 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s TGCAATTC 793s TGCAATTC 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s CTT 793s CTT 793s Processing line... 793s AAG 793s AAG 793s Processing line... 793s Processing line... 793s Processing line... 793s TGACT 793s TGACT 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s GTG 793s GTG 793s Processing line... 793s CAC 793s CAC 793s Processing line... 793s CAC 793s CAC 793s Processing line... 793s CAC 793s CAC 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s GGCCACCGGGAGG 793s GGCCACCGGGAGG 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s TGCAATTC 793s TGCAATTC 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s ACGGCCGCCACCCTCT 793s ACGGCCGCCACCCTCT 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s --- Summary --- 793s Read 1 reference strings 793s Checked 29 alignments, 0 edits 793s --------------- 793s PASSED 793s ALSO checking that bowtie2 and bowtie2-align match up 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 793s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 793s /usr/bin/bowtie2 --mp 7.4095732377906,2.5847847721105 --ma 3.03534389194298 --cp-ival 1 --cp-min 13 --rfg 6.00209318156257,12.4705618969154 --rdg 41.9864492983782 --score-min L,4.34740533983775,7.90672918924689 --gbar 5 --np 3 --trim5 6 --mm -k 7 --qseq -p 3 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 793s 123 reads; of these: 793s 123 (100.00%) were unpaired; of these: 793s 109 (88.62%) aligned 0 times 793s 6 (4.88%) aligned exactly 1 time 793s 8 (6.50%) aligned >1 times 793s 11.38% overall alignment rate 793s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 793s 123 reads; of these: 793s 123 (100.00%) were unpaired; of these: 793s 109 (88.62%) aligned 0 times 793s 6 (4.88%) aligned exactly 1 time 793s 8 (6.50%) aligned >1 times 793s 11.38% overall alignment rate 793s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 793s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 793s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 793s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 793s /usr/bin/bowtie2 --mp 7.4095732377906,2.5847847721105 --ma 3.03534389194298 --cp-ival 1 --cp-min 13 --rfg 6.00209318156257,12.4705618969154 --rdg 41.9864492983782 --score-min L,4.34740533983775,7.90672918924689 --gbar 5 --np 3 --trim5 6 --mm -k 7 --qseq -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_91_91_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 793s Warning: skipping read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 793s 123 reads; of these: 793s 123 (100.00%) were unpaired; of these: 793s 109 (88.62%) aligned 0 times 793s 6 (4.88%) aligned exactly 1 time 793s 8 (6.50%) aligned >1 times 793s 11.38% overall alignment rate 793s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 793s Flattened IUPAC characters 793s Mutating sequence Sim.pm.1 793s Introducing 6 SNPs, 2/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutating sequence Sim.pm.2 793s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutated reference genome to subject genome 793s SNPs introduced: 12 793s Reference gaps introduced: 3 793s Read gaps introduced: 0 793s Rearrangements introduced: 0 793s Created read sampler 793s Sampling 92 reads 793s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 793s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 793s parsing sequence Sim.pm.1... 793s parsing sequence Sim.pm.2... 793s Parsed 86 reference bases 793s *** Run 92 of 100 793s /usr/bin/bowtie2 --cp-min 6 --np 2 --norc -k 3 --local --cp-ival 1 --n-ceil 1.24498539153662,0.815542733446291 --mp 7.41022402135145,5.08561828559151 --trim3 7 --rfg 33.9970304429287 --rdg 45.8226136602099,18.8558372895914 --score-min L,4.23548312346268,9.87615733382915 --mm --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 793s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 793s Read 50 alignments... 793s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 793s Read 100 alignments... 793s 92 reads; of these: 793s 76 (82.61%) were paired; of these: 793s 76 (100.00%) aligned concordantly 0 times 793s 0 (0.00%) aligned concordantly exactly 1 time 793s 0 (0.00%) aligned concordantly >1 times 793s ---- 793s 76 pairs aligned concordantly 0 times; of these: 793s 0 (0.00%) aligned discordantly 1 time 793s ---- 793s 76 pairs aligned 0 times concordantly or discordantly; of these: 793s 152 mates make up the pairs; of these: 793s 152 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 16 (17.39%) were unpaired; of these: 793s 16 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 0.00% overall alignment rate 793s Read 150 alignments... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s --- Summary --- 793s Read 1 reference strings 793s Checked 0 alignments, 0 edits 793s --------------- 793s PASSED 793s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 793s /usr/bin/bowtie2 --cp-min 6 --np 2 --norc -k 3 --local --cp-ival 1 --n-ceil 1.24498539153662,0.815542733446291 --mp 7.41022402135145,5.08561828559151 --trim3 7 --rfg 33.9970304429287 --rdg 45.8226136602099,18.8558372895914 --score-min L,4.23548312346268,9.87615733382915 --mm --qseq -p 2 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 793s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 793s 92 reads; of these: 793s 76 (82.61%) were paired; of these: 793s 76 (100.00%) aligned concordantly 0 times 793s 0 (0.00%) aligned concordantly exactly 1 time 793s 0 (0.00%) aligned concordantly >1 times 793s ---- 793s 76 pairs aligned concordantly 0 times; of these: 793s 0 (0.00%) aligned discordantly 1 time 793s ---- 793s 76 pairs aligned 0 times concordantly or discordantly; of these: 793s 152 mates make up the pairs; of these: 793s 152 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 16 (17.39%) were unpaired; of these: 793s 16 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 0.00% overall alignment rate 793s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 793s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 793s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 793s /usr/bin/bowtie2 --cp-min 6 --np 2 --norc -k 3 --local --cp-ival 1 --n-ceil 1.24498539153662,0.815542733446291 --mp 7.41022402135145,5.08561828559151 --trim3 7 --rfg 33.9970304429287 --rdg 45.8226136602099,18.8558372895914 --score-min L,4.23548312346268,9.87615733382915 --mm --qseq -p 4 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 793s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 793s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (1) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 793s Warning: skipping read 'R_1_1_1_88_88_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping read 'R_1_1_1_88_88_1/1' because it was < 2 characters long 793s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read 'R_1_1_1_92_92_1/1' because it was < 2 characters long 793s 92 reads; of these: 793s 76 (82.61%) were paired; of these: 793s 76 (100.00%) aligned concordantly 0 times 793s 0 (0.00%) aligned concordantly exactly 1 time 793s 0 (0.00%) aligned concordantly >1 times 793s ---- 793s 76 pairs aligned concordantly 0 times; of these: 793s 0 (0.00%) aligned discordantly 1 time 793s ---- 793s 76 pairs aligned 0 times concordantly or discordantly; of these: 793s 152 mates make up the pairs; of these: 793s 152 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 16 (17.39%) were unpaired; of these: 793s 16 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 0.00% overall alignment rate 793s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 793s Flattened IUPAC characters 793s Mutating sequence Sim.pm.1 793s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutating sequence Sim.pm.2 793s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutated reference genome to subject genome 793s SNPs introduced: 9 793s Reference gaps introduced: 0 793s Read gaps introduced: 0 793s Rearrangements introduced: 0 793s Created read sampler 793s Sampling 74 reads 793s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 793s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 793s parsing sequence Sim.pm.1... 793s parsing sequence Sim.pm.2... 793s Parsed 86 reference bases 793s *** Run 93 of 100 793s /usr/bin/bowtie2 -R 1 --trim3 2 --mp 8.96471941052058,6.47190877008822 --cp-min 4 --local --cp-ival 2 --score-min L,7.49068677458371,6.97980411084525 --rfg 7.45519543611054,2.10284783865421 --gbar 8 -q -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.fastq -2 /tmp/Sim.pm.GP7sSa1l_2.fastq 793s Warning: skipping mate #1 of read '3' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read '3' because it was < 2 characters long 793s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read '14' because it was < 2 characters long 793s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read '28' because it was < 2 characters long 793s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read '36' because it was < 2 characters long 793s Warning: skipping mate #1 of read '42' because length (0) <= # seed mismatches (0) 793s Warning: skipping mate #1 of read '42' because it was < 2 characters long 793s Read 50 alignments... 793s Read 100 alignments... 793s 74 reads; of these: 793s 68 (91.89%) were paired; of these: 793s 68 (100.00%) aligned concordantly 0 times 793s 0 (0.00%) aligned concordantly exactly 1 time 793s 0 (0.00%) aligned concordantly >1 times 793s ---- 793s 68 pairs aligned concordantly 0 times; of these: 793s 0 (0.00%) aligned discordantly 1 time 793s ---- 793s 68 pairs aligned 0 times concordantly or discordantly; of these: 793s 136 mates make up the pairs; of these: 793s 136 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 6 (8.11%) were unpaired; of these: 793s 6 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 0.00% overall alignment rate 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s *** Run 94 of 100 793s /usr/bin/bowtie2 --gbar 7 --score-min L,8.81638570241294,7.39124378341051 --rdg 17.5199328005287 -i S,2.4404128777958,0.854115835204649 --trim5 5 --cp-min 3 --cp-ival 2 --ma 13.8705664388827 --nofw -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s --- Summary --- 793s Read 1 reference strings 793s Checked 0 alignments, 0 edits 793s --------------- 793s PASSED 793s Flattened IUPAC characters 793s Mutating sequence Sim.pm.1 793s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutating sequence Sim.pm.2 793s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutated reference genome to subject genome 793s SNPs introduced: 1 793s Reference gaps introduced: 0 793s Read gaps introduced: 1 793s Rearrangements introduced: 0 793s Created read sampler 793s Sampling 63 reads 793s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 793s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 793s parsing sequence Sim.pm.1... 793s parsing sequence Sim.pm.2... 793s Parsed 86 reference bases 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 793s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '9' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 793s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '10' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 793s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '12' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 793s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '23' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 793s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '30' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 793s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '37' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 793s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '41' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 793s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '45' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 793s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '55' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 793s 63 reads; of these: 793s 63 (100.00%) were unpaired; of these: 793s 51 (80.95%) aligned 0 times 793s 10 (15.87%) aligned exactly 1 time 793s 2 (3.17%) aligned >1 times 793s 19.05% overall alignment rate 793s Read 50 alignments... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s CGG 793s CGG 793s Processing line... 793s Processing line... 793s Processing line... 793s AATCAT 793s AATCAT 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s ATCTCAAA 793s ATCTCAAA 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s GACTGG 793s GACTGG 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s AGGGC 793s AGGGC 793s Processing line... 793s Processing line... 793s Processing line... 793s GCCACCGGGAGGC 793s GCCACCGGGAGGC 793s Processing line... 793s GCA 793s GCA 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s TGGAT 793s TGGAT 793s Processing line... 793s Processing line... 793s AATCAT 793s AATCAT 793s Processing line... 793s Processing line... 793s Processing line... 793s GTG 793s GTG 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s GCAATTC 793s GCAATTC 793s Processing line... 793s Processing line... 793s GACTGG 793s GACTGG 793s --- Summary --- 793s Read 1 reference strings 793s Checked 12 alignments, 0 edits 793s --------------- 793s PASSED 793s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 793s /usr/bin/bowtie2 --gbar 7 --score-min L,8.81638570241294,7.39124378341051 --rdg 17.5199328005287 -i S,2.4404128777958,0.854115835204649 --trim5 5 --cp-min 3 --cp-ival 2 --ma 13.8705664388827 --nofw -f -p 4 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 793s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '9' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 793s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '10' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 793s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '12' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 793s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '23' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 793s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '30' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 793s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '37' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 793s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '41' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 793s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '45' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 793s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '55' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 793s 63 reads; of these: 793s 63 (100.00%) were unpaired; of these: 793s 51 (80.95%) aligned 0 times 793s 10 (15.87%) aligned exactly 1 time 793s 2 (3.17%) aligned >1 times 793s 19.05% overall alignment rate 793s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 793s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 793s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 793s Flattened IUPAC characters 793s Mutating sequence Sim.pm.1 793s Introducing 5 SNPs, 1/0 ref/read gaps, and 1 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutating sequence Sim.pm.2 793s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutated reference genome to subject genome 793s SNPs introduced: 13 793s Reference gaps introduced: 1 793s Read gaps introduced: 0 793s Rearrangements introduced: 1 793s Created read sampler 793s Sampling 59 reads 793s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 793s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 793s parsing sequence Sim.pm.1... 793s parsing sequence Sim.pm.2... 793s Parsed 86 reference bases 793s *** Run 95 of 100 793s /usr/bin/bowtie2 --cp-min 3 --ma 9.16473138006505 --np 2 --norc --trim3 0 --cp-ival 2 -D 33 --nofw -a --score-min L,6.96937862383071,6.81497417961844 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 793s Warning: skipping read '33' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '33' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 793s Warning: skipping read '41' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '41' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 793s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '57' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 793s 59 reads; of these: 793s 59 (100.00%) were unpaired; of these: 793s 59 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 0.00% overall alignment rate 793s Read 50 alignments... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s --- Summary --- 793s Read 1 reference strings 793s Checked 0 alignments, 0 edits 793s --------------- 793s PASSED 793s Flattened IUPAC characters 793s Mutating sequence Sim.pm.1 793s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutating sequence Sim.pm.2 793s Introducing 8 SNPs, 0/0 ref/read gaps, and 1 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutated reference genome to subject genome 793s SNPs introduced: 13 793s Reference gaps introduced: 0 793s Read gaps introduced: 0 793s Rearrangements introduced: 2 793s Created read sampler 793s Sampling 147 reads 793s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 793s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 793s parsing sequence Sim.pm.1... 793s parsing sequence Sim.pm.2... 793s Parsed 86 reference bases 793s *** Run 96 of 100 793s /usr/bin/bowtie2 -i S,1.67733296732106,0.535327879946153 --trim5 4 -M 3 --cp-min 2 --score-min L,6.27802542207398,2.94355631815376 --rdg 44.3989666206353,15.6014962560158 --mm --cp-ival 3 --local --mp 3.14620327317495,1.27965467924748 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 793s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 793s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '22' because it was < 2 characters long 793s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '25' because it was < 2 characters long 793s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '30' because it was < 2 characters long 793s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '34' because it was < 2 characters long 793s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '38' because it was < 2 characters long 793s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '63' because it was < 2 characters long 793s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '67' because it was < 2 characters long 793s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '68' because it was < 2 characters long 793s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '69' because it was < 2 characters long 793s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '70' because it was < 2 characters long 793s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '71' because it was < 2 characters long 793s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '73' because it was < 2 characters long 793s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '76' because it was < 2 characters long 793s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '78' because it was < 2 characters long 793s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '79' because it was < 2 characters long 793s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '82' because it was < 2 characters long 793s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '90' because it was < 2 characters long 793s Warning: skipping read '106' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '106' because it was < 2 characters long 793s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '109' because it was < 2 characters long 793s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '110' because it was < 2 characters long 793s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '117' because it was < 2 characters long 793s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '119' because it was < 2 characters long 793s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '120' because it was < 2 characters long 793s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '123' because it was < 2 characters long 793s Warning: skipping read '128' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '128' because it was < 2 characters long 793s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '132' because it was < 2 characters long 793s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '133' because it was < 2 characters long 793s Warning: skipping read '134' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '134' because it was < 2 characters long 793s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '142' because it was < 2 characters long 793s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '146' because it was < 2 characters long 793s 147 reads; of these: 793s 147 (100.00%) were unpaired; of these: 793s 147 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 0.00% overall alignment rate 793s Read 50 alignments... 793s Read 100 alignments... 793s Read 150 alignments... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s --- Summary --- 793s Read 1 reference strings 793s Checked 0 alignments, 0 edits 793s --------------- 793s PASSED 793s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 793s /usr/bin/bowtie2 -i S,1.67733296732106,0.535327879946153 --trim5 4 -M 3 --cp-min 2 --score-min L,6.27802542207398,2.94355631815376 --rdg 44.3989666206353,15.6014962560158 --mm --cp-ival 3 --local --mp 3.14620327317495,1.27965467924748 -r -p 4 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 793s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 793s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '22' because it was < 2 characters long 793s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '25' because it was < 2 characters long 793s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '30' because it was < 2 characters long 793s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '34' because it was < 2 characters long 793s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '38' because it was < 2 characters long 793s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '63' because it was < 2 characters long 793s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '67' because it was < 2 characters long 793s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '68' because it was < 2 characters long 793s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '69' because it was < 2 characters long 793s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '70' because it was < 2 characters long 793s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '71' because it was < 2 characters long 793s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '73' because it was < 2 characters long 793s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '76' because it was < 2 characters long 793s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '78' because it was < 2 characters long 793s Warning: skipping read '79' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '79' because it was < 2 characters long 793s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '82' because it was < 2 characters long 793s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '90' because it was < 2 characters long 793s Warning: skipping read '106' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '106' because it was < 2 characters long 793s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '109' because it was < 2 characters long 793s Warning: skipping read '110' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '110' because it was < 2 characters long 793s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '117' because it was < 2 characters long 793s Warning: skipping read '119' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '119' because it was < 2 characters long 793s Warning: skipping read '120' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '120' because it was < 2 characters long 793s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '123' because it was < 2 characters long 793s Warning: skipping read '128' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '128' because it was < 2 characters long 793s Warning: skipping read '132' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '132' because it was < 2 characters long 793s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '133' because it was < 2 characters long 793s Warning: skipping read '134' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '134' because it was < 2 characters long 793s Warning: skipping read '142' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '142' because it was < 2 characters long 793s Warning: skipping read '146' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '146' because it was < 2 characters long 793s 147 reads; of these: 793s 147 (100.00%) were unpaired; of these: 793s 147 (100.00%) aligned 0 times 793s 0 (0.00%) aligned exactly 1 time 793s 0 (0.00%) aligned >1 times 793s 0.00% overall alignment rate 793s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 793s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 793s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 793s Flattened IUPAC characters 793s Mutating sequence Sim.pm.2 793s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutating sequence Sim.pm.1 793s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutated reference genome to subject genome 793s SNPs introduced: 1 793s Reference gaps introduced: 0 793s Read gaps introduced: 1 793s Rearrangements introduced: 0 793s Created read sampler 793s Sampling 38 reads 793s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fastq & /tmp/Sim.pm.GP7sSa1l_2.fastq 793s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 793s *** Run 97 of 100 793s /usr/bin/bowtie2 --cp-min 7 --ma 15.7309823055442 --np 2 -M 4 --trim5 5 --n-ceil 1.24498955594567,0.984523028454025 --cp-ival 1 --mp 7.97824220273205,2.62637236585917 --rfg 24.3348489000751,11.1100884896505 --score-min L,8.3597921666607,8.59855409938707 -q -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fastq 793s parsing sequence Sim.pm.1... 793s parsing sequence Sim.pm.2... 793s Parsed 86 reference bases 793s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 793s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '7' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 793s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '8' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 793s Warning: skipping read '16' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '16' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 793s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '23' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 793s 38 reads; of these: 793s 38 (100.00%) were unpaired; of these: 793s 25 (65.79%) aligned 0 times 793s 8 (21.05%) aligned exactly 1 time 793s 5 (13.16%) aligned >1 times 793s 34.21% overall alignment rate 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s TGCAATTCGAATCATGACTGGAT 793s TGCAATTCGAATCATGACTGGAT 793s Processing line... 793s Processing line... 793s CT 793s CT 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s AATTCGAATCATGACTGGATCTCAAA 793s AATTCGAATCATGACTGGATCTCAAA 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s TC 793s TC 793s Processing line... 793s Processing line... 793s Processing line... 793s CA 793s CA 793s Processing line... 793s Processing line... 793s AATTCGAATCATGACTGGATCTCAAA 793s AATTCGAATCATGACTGGATCTCAAA 793s Processing line... 793s ACTGGA 793s ACTGGA 793s Processing line... 793s AAT 793s AAT 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s AA 793s AA 793s Processing line... 793s Processing line... 793s Processing line... 793s Processing line... 793s TGGATCTCA 793s TGGATCTCA 793s Processing line... 793s AATCATGAC 793s AATCATGAC 793s Processing line... 793s GCAATTCGAATCATGACTGGATCT 793s GCAATTCGAATCATGACTGGATCT 793s Processing line... 793s TCGAATCATG 793s TCGAATCATG 793s --- Summary --- 793s Read 1 reference strings 793s Checked 13 alignments, 0 edits 793s --------------- 793s PASSED 793s Flattened IUPAC characters 793s Mutating sequence Sim.pm.2 793s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutating sequence Sim.pm.1 793s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 793s Finished SNPs 793s Finished ref gaps 793s Finished read gaps 793s Mutated reference genome to subject genome 793s SNPs introduced: 9 793s Reference gaps introduced: 1 793s Read gaps introduced: 0 793s Rearrangements introduced: 0 793s Created read sampler 793s Sampling 99 reads 793s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.raw & /tmp/Sim.pm.GP7sSa1l_2.raw 793s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 793s parsing sequence Sim.pm.1... 793s parsing sequence Sim.pm.2... 793s Parsed 86 reference bases 793s *** Run 98 of 100 793s /usr/bin/bowtie2 --mp 7.52976487671492,7.31837987111057 --cp-ival 3 --n-ceil 0.720759444993247,0.641396706234068 -a --mm --rdg 20.5228908147876,12.0955177033874 --score-min L,2.76772018906484,5.10152966977564 --gbar 1 -R 2 --ma 29.5860604573112 --cp-min 5 -i S,2.16131812227519 --trim5 1 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw 793s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 793s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 793s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '27' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 793s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '31' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 793s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 793s Warning: skipping read '43' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 793s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '70' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 793s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 793s Warning: skipping read '77' because it was < 2 characters long 793s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 793s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 794s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '82' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 794s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '83' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 794s 99 reads; of these: 794s 99 (100.00%) were unpaired; of these: 794s 78 (78.79%) aligned 0 times 794s 13 (13.13%) aligned exactly 1 time 794s 8 (8.08%) aligned >1 times 794s 21.21% overall alignment rate 794s Read 50 alignments... 794s Read 100 alignments... 794s Read 150 alignments... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s AAAGGG 794s AAAGGG 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s GGCCGCCA 794s GGCCGCCA 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s ATTCGAATCATGACTGGATCTCA 794s ATTCGAATCATGACTGGATCTCA 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CGG 794s CGG 794s Processing line... 794s CCG 794s CCG 794s Processing line... 794s CCG 794s CCG 794s Processing line... 794s CCG 794s CCG 794s Processing line... 794s CGG 794s CGG 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CTTTC 794s CTTTC 794s Processing line... 794s TT 794s TT 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s TT 794s TT 794s Processing line... 794s TT 794s TT 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CTTT 794s CTTT 794s Processing line... 794s AAAG 794s AAAG 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s GAATCATGACT 794s GAATCATGACT 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CTGGA 794s CTGGA 794s Processing line... 794s CAA 794s CAA 794s Processing line... 794s CAA 794s CAA 794s Processing line... 794s CAA 794s CAA 794s Processing line... 794s CAA 794s CAA 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s GCAATTCGAATCATG 794s GCAATTCGAATCATG 794s Processing line... 794s Processing line... 794s Processing line... 794s GT 794s GT 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s Processing line... 794s ATGACTGGATCTC 794s ATGACTGGATCTC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s TGTGCAATTCGAA 794s TGTGCAATTCGAA 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s TCATG 794s TCATG 794s Processing line... 794s CATGA 794s CATGA 794s Processing line... 794s Processing line... 794s Processing line... 794s CGGCCGCCACCCT 794s CGGCCGCCACCCT 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s ACTG 794s ACTG 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CGAATCATGACTGG 794s CGAATCATGACTGG 794s Processing line... 794s Processing line... 794s CATGACTGGATCTCAAAT 794s CATGACTGGATCTCAAAT 794s Processing line... 794s Processing line... 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s GG 794s GG 794s Processing line... 794s GG 794s GG 794s Processing line... 794s GG 794s GG 794s Processing line... 794s CC 794s CC 794s Processing line... 794s CC 794s CC 794s Processing line... 794s CC 794s CC 794s Processing line... 794s GG 794s GG 794s Processing line... 794s CC 794s CC 794s Processing line... 794s CC 794s CC 794s Processing line... 794s CC 794s CC 794s Processing line... 794s CC 794s CC 794s Processing line... 794s GG 794s GG 794s Processing line... 794s GG 794s GG 794s Processing line... 794s CC 794s CC 794s Processing line... 794s CC 794s CC 794s Processing line... 794s GG 794s GG 794s Processing line... 794s --- Summary --- 794s Read 1 reference strings 794s Checked 71 alignments, 0 edits 794s --------------- 794s PASSED 794s ALSO checking that bowtie2 and bowtie2-align match up 794s /usr/bin/bowtie2 --mp 7.52976487671492,7.31837987111057 --cp-ival 3 --n-ceil 0.720759444993247,0.641396706234068 -a --mm --rdg 20.5228908147876,12.0955177033874 --score-min L,2.76772018906484,5.10152966977564 --gbar 1 -R 2 --ma 29.5860604573112 --cp-min 5 -i S,2.16131812227519 --trim5 1 -r -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.als 794s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 794s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 794s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '27' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 794s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '31' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 794s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '43' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 794s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '70' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 794s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '77' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 794s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '82' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 794s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '83' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 794s 99 reads; of these: 794s 99 (100.00%) were unpaired; of these: 794s 78 (78.79%) aligned 0 times 794s 13 (13.13%) aligned exactly 1 time 794s 8 (8.08%) aligned >1 times 794s 21.21% overall alignment rate 794s diff -uw /tmp/Sim.pm.GP7sSa1l.als /tmp/Sim.pm.GP7sSa1l.debug.als 794s /usr/bin/bowtie2 --mp 7.52976487671492,7.31837987111057 --cp-ival 3 --n-ceil 0.720759444993247,0.641396706234068 -a --mm --rdg 20.5228908147876,12.0955177033874 --score-min L,2.76772018906484,5.10152966977564 --gbar 1 -R 2 --ma 29.5860604573112 --cp-min 5 -i S,2.16131812227519 --trim5 1 -r -p 4 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 794s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 794s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 794s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 794s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '27' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 794s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '31' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 794s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '43' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 794s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '70' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 794s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '77' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 794s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '82' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 794s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '83' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 794s 99 reads; of these: 794s 99 (100.00%) were unpaired; of these: 794s 78 (78.79%) aligned 0 times 794s 13 (13.13%) aligned exactly 1 time 794s 8 (8.08%) aligned >1 times 794s 21.21% overall alignment rate 794s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 794s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 794s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 794s /usr/bin/bowtie2 --mp 7.52976487671492,7.31837987111057 --cp-ival 3 --n-ceil 0.720759444993247,0.641396706234068 -a --mm --rdg 20.5228908147876,12.0955177033874 --score-min L,2.76772018906484,5.10152966977564 --gbar 1 -R 2 --ma 29.5860604573112 --cp-min 5 -i S,2.16131812227519 --trim5 1 -r -p 2 -x /tmp/Sim.pm.GP7sSa1l --reorder /tmp/Sim.pm.GP7sSa1l_1.raw | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 794s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 794s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 794s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 794s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '27' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 794s Warning: skipping read '31' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '31' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 794s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '43' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 794s Warning: skipping read '70' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '70' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 794s Warning: skipping read '77' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '77' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 794s Warning: skipping read '82' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '82' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 794s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '83' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 794s 99 reads; of these: 794s 99 (100.00%) were unpaired; of these: 794s 78 (78.79%) aligned 0 times 794s 13 (13.13%) aligned exactly 1 time 794s 8 (8.08%) aligned >1 times 794s 21.21% overall alignment rate 794s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 794s Flattened IUPAC characters 794s Mutating sequence Sim.pm.1 794s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 794s Finished SNPs 794s Finished ref gaps 794s Finished read gaps 794s Mutating sequence Sim.pm.2 794s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 794s Finished SNPs 794s Finished ref gaps 794s Finished read gaps 794s Mutated reference genome to subject genome 794s SNPs introduced: 3 794s Reference gaps introduced: 1 794s Read gaps introduced: 0 794s Rearrangements introduced: 0 794s Created read sampler 794s Sampling 138 reads 794s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.qseq & /tmp/Sim.pm.GP7sSa1l_2.qseq 794s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 794s parsing sequence Sim.pm.1... 794s parsing sequence Sim.pm.2... 794s Parsed 86 reference bases 794s *** Run 99 of 100 794s /usr/bin/bowtie2 --cp-min 5 --trim5 9 -M 8 --np 5 --norc --trim3 7 --local --cp-ival 1 -D 48 --nofw --mm --score-min L,4.57815442008112,2.90962354387995 --rfg 5.60032953462937 --rdg 32.7729538421617,9.79065244142221 --qseq -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq 794s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 794s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 794s Read 50 alignments... 794s 138 reads; of these: 794s 96 (69.57%) were paired; of these: 794s 96 (100.00%) aligned concordantly 0 times 794s 0 (0.00%) aligned concordantly exactly 1 time 794s 0 (0.00%) aligned concordantly >1 times 794s ---- 794s 96 pairs aligned concordantly 0 times; of these: 794s 0 (0.00%) aligned discordantly 1 time 794s ---- 794s 96 pairs aligned 0 times concordantly or discordantly; of these: 794s 192 mates make up the pairs; of these: 794s 192 (100.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 0 (0.00%) aligned >1 times 794s 42 (30.43%) were unpaired; of these: 794s 42 (100.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 0 (0.00%) aligned >1 times 794s 0.00% overall alignment rate 794s Read 100 alignments... 794s Read 150 alignments... 794s Read 200 alignments... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s --- Summary --- 794s Read 1 reference strings 794s Checked 0 alignments, 0 edits 794s --------------- 794s PASSED 794s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 794s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 794s /usr/bin/bowtie2 --cp-min 5 --trim5 9 -M 8 --np 5 --norc --trim3 7 --local --cp-ival 1 -D 48 --nofw --mm --score-min L,4.57815442008112,2.90962354387995 --rfg 5.60032953462937 --rdg 32.7729538421617,9.79065244142221 --qseq -p 3 -x /tmp/Sim.pm.GP7sSa1l -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 794s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 794s 138 reads; of these: 794s 96 (69.57%) were paired; of these: 794s 96 (100.00%) aligned concordantly 0 times 794s 0 (0.00%) aligned concordantly exactly 1 time 794s 0 (0.00%) aligned concordantly >1 times 794s ---- 794s 96 pairs aligned concordantly 0 times; of these: 794s 0 (0.00%) aligned discordantly 1 time 794s ---- 794s 96 pairs aligned 0 times concordantly or discordantly; of these: 794s 192 mates make up the pairs; of these: 794s 192 (100.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 0 (0.00%) aligned >1 times 794s 42 (30.43%) were unpaired; of these: 794s 42 (100.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 0 (0.00%) aligned >1 times 794s 0.00% overall alignment rate 794s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 794s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 794s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 794s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 794s /usr/bin/bowtie2 --cp-min 5 --trim5 9 -M 8 --np 5 --norc --trim3 7 --local --cp-ival 1 -D 48 --nofw --mm --score-min L,4.57815442008112,2.90962354387995 --rfg 5.60032953462937 --rdg 32.7729538421617,9.79065244142221 --qseq -p 3 -x /tmp/Sim.pm.GP7sSa1l --reorder -1 /tmp/Sim.pm.GP7sSa1l_1.qseq -2 /tmp/Sim.pm.GP7sSa1l_2.qseq | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.reord.als 794s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 794s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_81_81_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_86_86_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_90_90_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_100_100_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_108_108_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_115_115_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_119_119_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_128_128_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_129_129_1/1' because it was < 2 characters long 794s Warning: skipping read 'R_1_1_1_130_130_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 794s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read 'R_1_1_1_135_135_1/1' because it was < 2 characters long 794s 138 reads; of these: 794s 96 (69.57%) were paired; of these: 794s 96 (100.00%) aligned concordantly 0 times 794s 0 (0.00%) aligned concordantly exactly 1 time 794s 0 (0.00%) aligned concordantly >1 times 794s ---- 794s 96 pairs aligned concordantly 0 times; of these: 794s 0 (0.00%) aligned discordantly 1 time 794s ---- 794s 96 pairs aligned 0 times concordantly or discordantly; of these: 794s 192 mates make up the pairs; of these: 794s 192 (100.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 0 (0.00%) aligned >1 times 794s 42 (30.43%) were unpaired; of these: 794s 42 (100.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 0 (0.00%) aligned >1 times 794s 0.00% overall alignment rate 794s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als /tmp/Sim.pm.GP7sSa1l.px.reord.als 794s Flattened IUPAC characters 794s Mutating sequence Sim.pm.2 794s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 794s Finished SNPs 794s Finished ref gaps 794s Finished read gaps 794s Mutating sequence Sim.pm.1 794s Introducing 0 SNPs, 1/0 ref/read gaps, and 2 rearrangements 794s Finished SNPs 794s Finished ref gaps 794s Finished read gaps 794s Mutated reference genome to subject genome 794s SNPs introduced: 6 794s Reference gaps introduced: 1 794s Read gaps introduced: 0 794s Rearrangements introduced: 2 794s Created read sampler 794s Sampling 130 reads 794s Dumping reads to temporary files /tmp/Sim.pm.GP7sSa1l_1.fasta & /tmp/Sim.pm.GP7sSa1l_2.fasta 794s Parsing FASTA file /tmp/Sim.pm.GP7sSa1l.fa... 794s parsing sequence Sim.pm.1... 794s parsing sequence Sim.pm.2... 794s Parsed 86 reference bases 794s *** Run 100 of 100 794s /usr/bin/bowtie2 --ma 4.98057622758158 --cp-min 3 -M 5 --trim3 3 --cp-ival 2 -D 44 --rdg 32.2038317701433 --rfg 14.9310110477432,5.18662534088975 --score-min L,3.65510994926297,5.75976323409932 --gbar 6 -f -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta 794s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 794s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 794s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 794s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '14' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 794s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '18' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 794s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '20' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 794s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '22' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 794s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '33' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 794s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '45' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 794s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '50' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 794s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '53' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 794s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '58' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 794s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '60' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 794s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '66' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 794s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '67' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 794s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '92' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 794s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '94' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 794s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '108' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 794s Warning: skipping read '114' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '114' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 794s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '117' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 794s Warning: skipping read '121' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '121' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 794s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '126' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 794s 130 reads; of these: 794s 130 (100.00%) were unpaired; of these: 794s 91 (70.00%) aligned 0 times 794s 23 (17.69%) aligned exactly 1 time 794s 16 (12.31%) aligned >1 times 794s 30.00% overall alignment rate 794s Read 50 alignments... 794s Read 100 alignments... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CCGCCACCCTCTTT 794s CCGCCACCCTCTTT 794s Processing line... 794s Processing line... 794s TC 794s TC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s TGTGCAATTCGAATCATG 794s TGTGCAATTCGAATCATG 794s Processing line... 794s Processing line... 794s Processing line... 794s TGTGCAATT 794s TGTGCAATT 794s Processing line... 794s Processing line... 794s Processing line... 794s GC 794s GC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s TGGATCTCA 794s TGGATCTCA 794s Processing line... 794s Processing line... 794s Processing line... 794s GC 794s GC 794s Processing line... 794s Processing line... 794s Processing line... 794s GCCACCGGGAG 794s GCCACCGGGAG 794s Processing line... 794s CAATTCGAATCATGACT 794s CAATTCGAATCATGACT 794s Processing line... 794s GCCACCGGGAGGC 794s GCCACCGGGAGGC 794s Processing line... 794s AACGGCCGCCACCCTCTTTCCCG 794s AACGGCCGCCACCCTCTTTCCCG 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s GAGGC 794s GAGGC 794s Processing line... 794s Processing line... 794s AAC 794s AAC 794s Processing line... 794s Processing line... 794s Processing line... 794s /usr/bin/bowtie2 --ma 4.98057622758158 --cp-min 3 -M 5 --trim3 3 --cp-ival 2 -D 44 --rdg 32.2038317701433 --rfg 14.9310110477432,5.18662534088975 --score-min L,3.65510994926297,5.75976323409932 --gbar 6 -f -p 3 -x /tmp/Sim.pm.GP7sSa1l /tmp/Sim.pm.GP7sSa1l_1.fasta | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CGAATC 794s CGAATC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CCACCCTCTTTC 794s CCACCCTCTTTC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s ATTCGAATCA 794s ATTCGAATCA 794s Processing line... 794s ATGACTGGA 794s ATGACTGGA 794s Processing line... 794s Processing line... 794s Processing line... 794s GGC 794s GGC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CG 794s CG 794s Processing line... 794s TGCAATTCG 794s TGCAATTCG 794s Processing line... 794s Processing line... 794s Processing line... 794s CCT 794s CCT 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s GCAATTCGAAT 794s GCAATTCGAAT 794s Processing line... 794s GCC 794s GCC 794s Processing line... 794s TC 794s TC 794s Processing line... 794s AA 794s AA 794s Processing line... 794s Processing line... 794s GTGCAATTC 794s GTGCAATTC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CAC 794s CAC 794s Processing line... 794s Processing line... 794s GG 794s GG 794s Processing line... 794s TGGATCTCA 794s TGGATCTCA 794s Processing line... 794s AATTCGAATCATGACTGGATCTC 794s AATTCGAATCATGACTGGATCTC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CGGCCGCCACCCTCT 794s CGGCCGCCACCCTCT 794s Processing line... 794s Processing line... 794s CT 794s CT 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s TGTGCAATTCGAATCATGACTGGATCT 794s TGTGCAATTCGAATCATGACTGGATCT 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s GGA 794s GGA 794s Processing line... 794s Processing line... 794s GCC 794s GCC 794s Processing line... 794s CAATTCGAATCATGACTG 794s CAATTCGAATCATGACTG 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CG 794s CG 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s AATCATG 794s AATCATG 794s Processing line... 794s Processing line... 794s CGGG 794s CGGG 794s --- Summary --- 794s Read 1 reference strings 794s Checked 39 alignments, 0 edits 794s --------------- 794s PASSED 794s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 794s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 794s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 794s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 794s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '14' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 794s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '18' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 794s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '20' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 794s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '22' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 794s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '33' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 794s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '45' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 794s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '50' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 794s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '53' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 794s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '58' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 794s Warning: skipping read '60' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '60' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 794s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '66' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 794s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '67' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 794s Warning: skipping read '92' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '92' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 794s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '94' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 794s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '108' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 794s Warning: skipping read '114' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '114' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 794s Warning: skipping read '117' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '117' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 794s Warning: skipping read '121' because length (1) <= # seed mismatches (0) 794s Warning: skipping read '121' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 794s Warning: skipping read '126' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '126' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 794s 130 reads; of these: 794s 130 (100.00%) were unpaired; of these: 794s 91 (70.00%) aligned 0 times 794s 23 (17.69%) aligned exactly 1 time 794s 16 (12.31%) aligned >1 times 794s 30.00% overall alignment rate 794s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.px.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.px.als.sorted 794s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.GP7sSa1l.debug.als | grep -v '^@PG' > /tmp/Sim.pm.GP7sSa1l.debug.als.sorted 794s Created DNA generator 794s N frac: 0.026 794s IUPAC frac: 0.009 794s AT/ACGT frac: 0.547 794s A/AT frac: 0.610 794s C/CG frac: 0.700 794s Generating 2 references 794s Generated reference 'Sim.pm.1' of untrimmed length 71, trimmed length 33 794s Generated reference 'Sim.pm.2' of untrimmed length 115, trimmed length 45 794s Wrote references to /tmp/Sim.pm.ZMWIC0u_.fa 794s A: 23 794s C: 21 794s G: 7 794s N: 4 794s S: 1 794s T: 22 794s Executing: /usr/bin/bowtie2-build --packed --dcv 4096 --threads 2 --offrate 4 --large-index /tmp/Sim.pm.ZMWIC0u_.fa /tmp/Sim.pm.ZMWIC0u_ 794s diff -uw /tmp/Sim.pm.GP7sSa1l.debug.als.sorted /tmp/Sim.pm.GP7sSa1l.px.als.sorted 794s *** TEST CASE *** 794s Settings: 794s Output files: "/tmp/Sim.pm.ZMWIC0u_.*.bt2l" 794s Line rate: 7 (line is 128 bytes) 794s Lines per side: 1 (side is 128 bytes) 794s Offset rate: 4 (one in 16) 794s FTable chars: 10 794s Strings: packed 794s Max bucket size: default 794s Max bucket size, sqrt multiplier: default 794s Max bucket size, len divisor: 8 794s Difference-cover sample period: 4096 794s Endianness: little 794s Actual local endianness: little 794s Sanity checking: disabled 794s Assertions: disabled 794s Random seed: 0 794s Sizeofs: void*:8, int:4, long:8, size_t:8 794s Input files DNA, FASTA: 794s /tmp/Sim.pm.ZMWIC0u_.fa 794s Reading reference sizes 794s Building a LARGE index 794s Time reading reference sizes: 00:00:00 794s Calculating joined length 794s Writing header 794s Reserving space for joined string 794s Joining reference sequences 794s Time to join reference sequences: 00:00:00 794s bmax according to bmaxDivN setting: 9 794s Using parameters --bmax 7 --dcv 4096 794s Doing ahead-of-time memory usage test 794s Passed! Constructing with these parameters: --bmax 7 --dcv 4096 --packed 794s Constructing suffix-array element generator 794s Building DifferenceCoverSample 794s Building sPrime 794s Building sPrimeOrder 794s V-Sorting samples 794s V-Sorting samples time: 00:00:00 794s Allocating rank array 794s Ranking v-sort output 794s Ranking v-sort output time: 00:00:00 794s Invoking Larsson-Sadakane on ranks 794s Invoking Larsson-Sadakane on ranks time: 00:00:00 794s Sanity-checking and returning 794s Building samples 794s Reserving space for 26 sample suffixes 794s Generating random suffixes 794s QSorting 26 sample offsets, eliminating duplicates 794s QSorting sample offsets, eliminating duplicates time: 00:00:00 794s Multikey QSorting 22 samples 794s (Using difference cover) 794s Multikey QSorting samples time: 00:00:00 794s Calculating bucket sizes 794s Splitting and merging 794s Splitting and merging time: 00:00:00 794s Split 1, merged 11; iterating... 794s Splitting and merging 794s Splitting and merging time: 00:00:00 794s Split 1, merged 0; iterating... 794s Splitting and merging 794s Splitting and merging time: 00:00:00 794s Split 1, merged 1; iterating... 794s Splitting and merging 794s Splitting and merging time: 00:00:00 794s Avg bucket size: 4.69231 (target: 6) 794s Converting suffix-array elements to index image 794s Allocating ftab, absorbFtab 794s Entering Ebwt loop 794s Getting block 1 of 13 794s Reserving size (7) for bucket 1 794s Calculating Z arrays for bucket 1 794s Entering block accumulator loop for bucket 1: 794s bucket 1: 10% 794s bucket 1: 20% 794s bucket 1: 30% 794s bucket 1: 40% 794s bucket 1: 50% 794s bucket 1: 60% 794s bucket 1: 70% 794s bucket 1: 80% 794s bucket 1: 90% 794s bucket 1: 100% 794s Sorting block of length 5 for bucket 1 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 6 for bucket 1 794s Getting block 2 of 13 794s Reserving size (7) for bucket 2 794s Calculating Z arrays for bucket 2 794s Entering block accumulator loop for bucket 2: 794s bucket 2: 10% 794s bucket 2: 20% 794s bucket 2: 30% 794s bucket 2: 40% 794s bucket 2: 50% 794s bucket 2: 60% 794s bucket 2: 70% 794s bucket 2: 80% 794s bucket 2: 90% 794s bucket 2: 100% 794s Sorting block of length 6 for bucket 2 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 2 794s Getting block 3 of 13 794s Reserving size (7) for bucket 3 794s Calculating Z arrays for bucket 3 794s Entering block accumulator loop for bucket 3: 794s bucket 3: 10% 794s bucket 3: 20% 794s bucket 3: 30% 794s bucket 3: 40% 794s bucket 3: 50% 794s bucket 3: 60% 794s bucket 3: 70% 794s bucket 3: 80% 794s bucket 3: 90% 794s bucket 3: 100% 794s Sorting block of length 5 for bucket 3 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 6 for bucket 3 794s Getting block 4 of 13 794s Reserving size (7) for bucket 4 794s Calculating Z arrays for bucket 4 794s Entering block accumulator loop for bucket 4: 794s bucket 4: 10% 794s bucket 4: 20% 794s bucket 4: 30% 794s bucket 4: 40% 794s bucket 4: 50% 794s bucket 4: 60% 794s bucket 4: 70% 794s bucket 4: 80% 794s bucket 4: 90% 794s bucket 4: 100% 794s Sorting block of length 6 for bucket 4 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 4 794s Getting block 5 of 13 794s Reserving size (7) for bucket 5 794s Calculating Z arrays for bucket 5 794s Entering block accumulator loop for bucket 5: 794s bucket 5: 10% 794s bucket 5: 20% 794s bucket 5: 30% 794s bucket 5: 40% 794s bucket 5: 50% 794s bucket 5: 60% 794s bucket 5: 70% 794s bucket 5: 80% 794s bucket 5: 90% 794s bucket 5: 100% 794s Sorting block of length 3 for bucket 5 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 4 for bucket 5 794s Getting block 6 of 13 794s Reserving size (7) for bucket 6 794s Calculating Z arrays for bucket 6 794s Entering block accumulator loop for bucket 6: 794s bucket 6: 10% 794s bucket 6: 20% 794s bucket 6: 30% 794s bucket 6: 40% 794s bucket 6: 50% 794s bucket 6: 60% 794s bucket 6: 70% 794s bucket 6: 80% 794s bucket 6: 90% 794s bucket 6: 100% 794s Sorting block of length 3 for bucket 6 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 4 for bucket 6 794s Getting block 7 of 13 794s Reserving size (7) for bucket 7 794s Calculating Z arrays for bucket 7 794s Entering block accumulator loop for bucket 7: 794s bucket 7: 10% 794s bucket 7: 20% 794s bucket 7: 30% 794s bucket 7: 40% 794s bucket 7: 50% 794s bucket 7: 60% 794s bucket 7: 70% 794s bucket 7: 80% 794s bucket 7: 90% 794s bucket 7: 100% 794s Sorting block of length 6 for bucket 7 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 7 794s Getting block 8 of 13 794s Reserving size (7) for bucket 8 794s Calculating Z arrays for bucket 8 794s Entering block accumulator loop for bucket 8: 794s bucket 8: 10% 794s bucket 8: 20% 794s bucket 8: 30% 794s bucket 8: 40% 794s bucket 8: 50% 794s bucket 8: 60% 794s bucket 8: 70% 794s bucket 8: 80% 794s bucket 8: 90% 794s bucket 8: 100% 794s Sorting block of length 5 for bucket 8 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 6 for bucket 8 794s Getting block 9 of 13 794s Reserving size (7) for bucket 9 794s Calculating Z arrays for bucket 9 794s Entering block accumulator loop for bucket 9: 794s bucket 9: 10% 794s bucket 9: 20% 794s bucket 9: 30% 794s bucket 9: 40% 794s bucket 9: 50% 794s bucket 9: 60% 794s bucket 9: 70% 794s bucket 9: 80% 794s bucket 9: 90% 794s bucket 9: 100% 794s Sorting block of length 2 for bucket 9 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 3 for bucket 9 794s Getting block 10 of 13 794s Reserving size (7) for bucket 10 794s Calculating Z arrays for bucket 10 794s Entering block accumulator loop for bucket 10: 794s bucket 10: 10% 794s bucket 10: 20% 794s bucket 10: 30% 794s bucket 10: 40% 794s bucket 10: 50% 794s bucket 10: 60% 794s bucket 10: 70% 794s bucket 10: 80% 794s bucket 10: 90% 794s bucket 10: 100% 794s Sorting block of length 5 for bucket 10 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 6 for bucket 10 794s Getting block 11 of 13 794s Reserving size (7) for bucket 11 794s Calculating Z arrays for bucket 11 794s Entering block accumulator loop for bucket 11: 794s bucket 11: 10% 794s bucket 11: 20% 794s bucket 11: 30% 794s bucket 11: 40% 794s bucket 11: 50% 794s bucket 11: 60% 794s bucket 11: 70% 794s bucket 11: 80% 794s bucket 11: 90% 794s bucket 11: 100% 794s Sorting block of length 4 for bucket 11 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 5 for bucket 11 794s Getting block 12 of 13 794s Reserving size (7) for bucket 12 794s Calculating Z arrays for bucket 12 794s Entering block accumulator loop for bucket 12: 794s bucket 12: 10% 794s bucket 12: 20% 794s bucket 12: 30% 794s bucket 12: 40% 794s bucket 12: 50% 794s bucket 12: 60% 794s bucket 12: 70% 794s bucket 12: 80% 794s bucket 12: 90% 794s bucket 12: 100% 794s Sorting block of length 5 for bucket 12 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 6 for bucket 12 794s Getting block 13 of 13 794s Reserving size (7) for bucket 13 794s Calculating Z arrays for bucket 13 794s Entering block accumulator loop for bucket 13: 794s bucket 13: 10% 794s bucket 13: 20% 794s bucket 13: 30% 794s bucket 13: 40% 794s bucket 13: 50% 794s bucket 13: 60% 794s bucket 13: 70% 794s bucket 13: 80% 794s bucket 13: 90% 794s bucket 13: 100% 794s Sorting block of length 6 for bucket 13 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 13 794s Exited Ebwt loop 794s fchr[A]: 0 794s fchr[C]: 23 794s fchr[G]: 44 794s fchr[T]: 51 794s fchr[$]: 73 794s Exiting Ebwt::buildToDisk() 794s Returning from initFromVector 794s Wrote 8389179 bytes to primary EBWT file: /tmp/Sim.pm.ZMWIC0u_.1.bt2l.tmp 794s Wrote 44 bytes to secondary EBWT file: /tmp/Sim.pm.ZMWIC0u_.2.bt2l.tmp 794s Re-opening _in1 and _in2 as input streams 794s Returning from Ebwt constructor 794s Headers: 794s len: 73 794s bwtLen: 74 794s sz: 19 794s bwtSz: 19 794s lineRate: 7 794s offRate: 4 794s offMask: 0xfffffffffffffff0 794s ftabChars: 10 794s eftabLen: 20 794s eftabSz: 160 794s ftabLen: 1048577 794s ftabSz: 8388616 794s offsLen: 5 794s offsSz: 40 794s lineSz: 128 794s sideSz: 128 794s sideBwtSz: 96 794s sideBwtLen: 384 794s numSides: 1 794s numLines: 1 794s ebwtTotLen: 128 794s ebwtTotSz: 128 794s color: 0 794s reverse: 0 794s Total time for call to driver() for forward index: 00:00:00 794s Reading reference sizes 794s Time reading reference sizes: 00:00:00 794s Calculating joined length 794s Writing header 794s Reserving space for joined string 794s Joining reference sequences 794s Time to join reference sequences: 00:00:00 794s Time to reverse reference sequence: 00:00:00 794s bmax according to bmaxDivN setting: 9 794s Using parameters --bmax 7 --dcv 4096 794s Doing ahead-of-time memory usage test 794s Passed! Constructing with these parameters: --bmax 7 --dcv 4096 --packed 794s Constructing suffix-array element generator 794s Building DifferenceCoverSample 794s Building sPrime 794s Building sPrimeOrder 794s V-Sorting samples 794s V-Sorting samples time: 00:00:00 794s Allocating rank array 794s Ranking v-sort output 794s Ranking v-sort output time: 00:00:00 794s Invoking Larsson-Sadakane on ranks 794s Invoking Larsson-Sadakane on ranks time: 00:00:00 794s Sanity-checking and returning 794s Building samples 794s Reserving space for 26 sample suffixes 794s Generating random suffixes 794s QSorting 26 sample offsets, eliminating duplicates 794s QSorting sample offsets, eliminating duplicates time: 00:00:00 794s Multikey QSorting 22 samples 794s (Using difference cover) 794s Multikey QSorting samples time: 00:00:00 794s Calculating bucket sizes 794s Splitting and merging 794s Splitting and merging time: 00:00:00 794s Avg bucket size: 4.28571 (target: 6) 794s Converting suffix-array elements to index image 794s Allocating ftab, absorbFtab 794s Entering Ebwt loop 794s Getting block 1 of 14 794s Reserving size (7) for bucket 1 794s Calculating Z arrays for bucket 1 794s Entering block accumulator loop for bucket 1: 794s bucket 1: 10% 794s bucket 1: 20% 794s bucket 1: 30% 794s bucket 1: 40% 794s bucket 1: 50% 794s bucket 1: 60% 794s bucket 1: 70% 794s bucket 1: 80% 794s bucket 1: 90% 794s bucket 1: 100% 794s Sorting block of length 4 for bucket 1 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 5 for bucket 1 794s Getting block 2 of 14 794s Reserving size (7) for bucket 2 794s Calculating Z arrays for bucket 2 794s Entering block accumulator loop for bucket 2: 794s bucket 2: 10% 794s bucket 2: 20% 794s bucket 2: 30% 794s bucket 2: 40% 794s bucket 2: 50% 794s bucket 2: 60% 794s bucket 2: 70% 794s bucket 2: 80% 794s bucket 2: 90% 794s bucket 2: 100% 794s Sorting block of length 5 for bucket 2 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 6 for bucket 2 794s Getting block 3 of 14 794s Reserving size (7) for bucket 3 794s Calculating Z arrays for bucket 3 794s Entering block accumulator loop for bucket 3: 794s bucket 3: 10% 794s bucket 3: 20% 794s bucket 3: 30% 794s bucket 3: 40% 794s bucket 3: 50% 794s bucket 3: 60% 794s bucket 3: 70% 794s bucket 3: 80% 794s bucket 3: 90% 794s bucket 3: 100% 794s Sorting block of length 5 for bucket 3 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 6 for bucket 3 794s Getting block 4 of 14 794s Reserving size (7) for bucket 4 794s Calculating Z arrays for bucket 4 794s Entering block accumulator loop for bucket 4: 794s bucket 4: 10% 794s bucket 4: 20% 794s bucket 4: 30% 794s bucket 4: 40% 794s bucket 4: 50% 794s bucket 4: 60% 794s bucket 4: 70% 794s bucket 4: 80% 794s bucket 4: 90% 794s bucket 4: 100% 794s Sorting block of length 6 for bucket 4 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 4 794s Getting block 5 of 14 794s Reserving size (7) for bucket 5 794s Calculating Z arrays for bucket 5 794s Entering block accumulator loop for bucket 5: 794s bucket 5: 10% 794s bucket 5: 20% 794s bucket 5: 30% 794s bucket 5: 40% 794s bucket 5: 50% 794s bucket 5: 60% 794s bucket 5: 70% 794s bucket 5: 80% 794s bucket 5: 90% 794s bucket 5: 100% 794s Sorting block of length 1 for bucket 5 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 2 for bucket 5 794s Getting block 6 of 14 794s Reserving size (7) for bucket 6 794s Calculating Z arrays for bucket 6 794s Entering block accumulator loop for bucket 6: 794s bucket 6: 10% 794s bucket 6: 20% 794s bucket 6: 30% 794s bucket 6: 40% 794s bucket 6: 50% 794s bucket 6: 60% 794s bucket 6: 70% 794s bucket 6: 80% 794s bucket 6: 90% 794s bucket 6: 100% 794s Sorting block of length 6 for bucket 6 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 6 794s Getting block 7 of 14 794s Reserving size (7) for bucket 7 794s Calculating Z arrays for bucket 7 794s Entering block accumulator loop for bucket 7: 794s bucket 7: 10% 794s bucket 7: 20% 794s bucket 7: 30% 794s bucket 7: 40% 794s bucket 7: 50% 794s bucket 7: 60% 794s bucket 7: 70% 794s bucket 7: 80% 794s bucket 7: 90% 794s bucket 7: 100% 794s Sorting block of length 6 for bucket 7 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 7 794s Getting block 8 of 14 794s Reserving size (7) for bucket 8 794s Calculating Z arrays for bucket 8 794s Entering block accumulator loop for bucket 8: 794s bucket 8: 10% 794s bucket 8: 20% 794s bucket 8: 30% 794s bucket 8: 40% 794s bucket 8: 50% 794s bucket 8: 60% 794s bucket 8: 70% 794s bucket 8: 80% 794s bucket 8: 90% 794s bucket 8: 100% 794s Sorting block of length 2 for bucket 8 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 3 for bucket 8 794s Getting block 9 of 14 794s Reserving size (7) for bucket 9 794s Calculating Z arrays for bucket 9 794s Entering block accumulator loop for bucket 9: 794s bucket 9: 10% 794s bucket 9: 20% 794s bucket 9: 30% 794s bucket 9: 40% 794s bucket 9: 50% 794s bucket 9: 60% 794s bucket 9: 70% 794s bucket 9: 80% 794s bucket 9: 90% 794s bucket 9: 100% 794s Sorting block of length 6 for bucket 9 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 9 794s Getting block 10 of 14 794s Reserving size (7) for bucket 10 794s Calculating Z arrays for bucket 10 794s Entering block accumulator loop for bucket 10: 794s bucket 10: 10% 794s bucket 10: 20% 794s bucket 10: 30% 794s bucket 10: 40% 794s bucket 10: 50% 794s bucket 10: 60% 794s bucket 10: 70% 794s bucket 10: 80% 794s bucket 10: 90% 794s bucket 10: 100% 794s Sorting block of length 1 for bucket 10 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 2 for bucket 10 794s Getting block 11 of 14 794s Reserving size (7) for bucket 11 794s Calculating Z arrays for bucket 11 794s Entering block accumulator loop for bucket 11: 794s bucket 11: 10% 794s bucket 11: 20% 794s bucket 11: 30% 794s bucket 11: 40% 794s bucket 11: 50% 794s bucket 11: 60% 794s bucket 11: 70% 794s bucket 11: 80% 794s bucket 11: 90% 794s bucket 11: 100% 794s Sorting block of length 6 for bucket 11 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 11 794s Getting block 12 of 14 794s Reserving size (7) for bucket 12 794s Calculating Z arrays for bucket 12 794s Entering block accumulator loop for bucket 12: 794s bucket 12: 10% 794s bucket 12: 20% 794s bucket 12: 30% 794s bucket 12: 40% 794s bucket 12: 50% 794s bucket 12: 60% 794s bucket 12: 70% 794s bucket 12: 80% 794s bucket 12: 90% 794s bucket 12: 100% 794s Sorting block of length 6 for bucket 12 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 7 for bucket 12 794s Getting block 13 of 14 794s Reserving size (7) for bucket 13 794s Calculating Z arrays for bucket 13 794s Entering block accumulator loop for bucket 13: 794s bucket 13: 10% 794s bucket 13: 20% 794s bucket 13: 30% 794s bucket 13: 40% 794s bucket 13: 50% 794s bucket 13: 60% 794s bucket 13: 70% 794s bucket 13: 80% 794s bucket 13: 90% 794s bucket 13: 100% 794s Sorting block of length 4 for bucket 13 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 5 for bucket 13 794s Getting block 14 of 14 794s Reserving size (7) for bucket 14 794s Calculating Z arrays for bucket 14 794s Entering block accumulator loop for bucket 14: 794s bucket 14: 10% 794s bucket 14: 20% 794s bucket 14: 30% 794s bucket 14: 40% 794s bucket 14: 50% 794s bucket 14: 60% 794s bucket 14: 70% 794s bucket 14: 80% 794s bucket 14: 90% 794s bucket 14: 100% 794s Sorting block of length 2 for bucket 14 794s (Using difference cover) 794s Sorting block time: 00:00:00 794s Returning block of 3 for bucket 14 794s Exited Ebwt loop 794s fchr[A]: 0 794s fchr[C]: 23 794s fchr[G]: 44 794s fchr[T]: 51 794s fchr[$]: 73 794s Exiting Ebwt::buildToDisk() 794s Returning from initFromVector 794s Wrote 8389179 bytes to primary EBWT file: /tmp/Sim.pm.ZMWIC0u_.rev.1.bt2l.tmp 794s Wrote 44 bytes to secondary EBWT file: /tmp/Sim.pm.ZMWIC0u_.rev.2.bt2l.tmp 794s Re-opening _in1 and _in2 as input streams 794s Returning from Ebwt constructor 794s Headers: 794s len: 73 794s bwtLen: 74 794s sz: 19 794s bwtSz: 19 794s lineRate: 7 794s offRate: 4 794s offMask: 0xfffffffffffffff0 794s ftabChars: 10 794s eftabLen: 20 794s eftabSz: 160 794s ftabLen: 1048577 794s ftabSz: 8388616 794s offsLen: 5 794s offsSz: 40 794s lineSz: 128 794s sideSz: 128 794s sideBwtSz: 96 794s sideBwtLen: 384 794s numSides: 1 794s numLines: 1 794s ebwtTotLen: 128 794s ebwtTotSz: 128 794s color: 0 794s reverse: 1 794s Total time for backward call to driver() for mirror index: 00:00:00 794s *** Run 1 of 100 794s /usr/bin/bowtie2 --cp-ival 1 --local --n-ceil 0.0226642333094309,1.04385828726364 --mp 6.65486933694402,3.42090475036619 -N 1 -L23 --mm --score-min L,8.04692647465912,9.74108020122713 --rfg 37.8618070079263,11.9474667299235 --cp-min 4 --large-index -k 3 -i S,1.59174837092804,2.43640609136527 --np 2 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 794s Renaming /tmp/Sim.pm.ZMWIC0u_.3.bt2l.tmp to /tmp/Sim.pm.ZMWIC0u_.3.bt2l 794s Renaming /tmp/Sim.pm.ZMWIC0u_.4.bt2l.tmp to /tmp/Sim.pm.ZMWIC0u_.4.bt2l 794s Renaming /tmp/Sim.pm.ZMWIC0u_.1.bt2l.tmp to /tmp/Sim.pm.ZMWIC0u_.1.bt2l 794s Renaming /tmp/Sim.pm.ZMWIC0u_.2.bt2l.tmp to /tmp/Sim.pm.ZMWIC0u_.2.bt2l 794s Renaming /tmp/Sim.pm.ZMWIC0u_.rev.1.bt2l.tmp to /tmp/Sim.pm.ZMWIC0u_.rev.1.bt2l 794s Renaming /tmp/Sim.pm.ZMWIC0u_.rev.2.bt2l.tmp to /tmp/Sim.pm.ZMWIC0u_.rev.2.bt2l 794s Built nucleotide index '/tmp/Sim.pm.ZMWIC0u_' 794s Flattened IUPAC characters 794s Mutating sequence Sim.pm.2 794s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 794s Finished SNPs 794s Finished ref gaps 794s Finished read gaps 794s Mutating sequence Sim.pm.1 794s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 794s Finished SNPs 794s Finished ref gaps 794s Finished read gaps 794s Mutated reference genome to subject genome 794s SNPs introduced: 6 794s Reference gaps introduced: 0 794s Read gaps introduced: 0 794s Rearrangements introduced: 0 794s Created read sampler 794s Sampling 99 reads 794s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 794s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 794s parsing sequence Sim.pm.1... 794s parsing sequence Sim.pm.2... 794s Parsed 78 reference bases 794s Warning: skipping mate #2 of read '33' because length (1) <= # seed mismatches (1) 794s Warning: skipping mate #2 of read '33' because it was < 2 characters long 794s Read 50 alignments... 794s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (1) 794s Warning: skipping mate #1 of read '75' because it was < 2 characters long 794s Read 100 alignments... 794s 99 reads; of these: 794s 99 (100.00%) were paired; of these: 794s 99 (100.00%) aligned concordantly 0 times 794s 0 (0.00%) aligned concordantly exactly 1 time 794s 0 (0.00%) aligned concordantly >1 times 794s ---- 794s 99 pairs aligned concordantly 0 times; of these: 794s 0 (0.00%) aligned discordantly 1 time 794s ---- 794s 99 pairs aligned 0 times concordantly or discordantly; of these: 794s 198 mates make up the pairs; of these: 794s 198 (100.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 0 (0.00%) aligned >1 times 794s 0.00% overall alignment rate 794s Read 150 alignments... 794s Read 200 alignments... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s --- Summary --- 794s Read 1 reference strings 794s Checked 0 alignments, 0 edits 794s --------------- 794s PASSED 794s Flattened IUPAC characters 794s Mutating sequence Sim.pm.2 794s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 794s Finished SNPs 794s Finished ref gaps 794s Finished read gaps 794s Mutating sequence Sim.pm.1 794s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 794s Finished SNPs 794s Finished ref gaps 794s Finished read gaps 794s Mutated reference genome to subject genome 794s SNPs introduced: 6 794s Reference gaps introduced: 0 794s Read gaps introduced: 0 794s Rearrangements introduced: 1 794s Created read sampler 794s Sampling 39 reads 794s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 794s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 794s parsing sequence Sim.pm.1... 794s parsing sequence Sim.pm.2... 794s Parsed 78 reference bases 794s *** Run 2 of 100 794s /usr/bin/bowtie2 --cp-min 7 --large-index -R 2 --trim5 8 -i L,0.1209547034377,0.301705810076089 --cp-ival 1 -D 28 --nofw --mp 7.36994422247878,2.75023352670011 --trim3 7 --score-min L,1.37057882756889,6.72360711056115 --rdg 10.075879813847,2.38623908200782 --rfg 48.2699867803365 -a --mm -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 794s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 794s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '4' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 794s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '9' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 794s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '12' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 794s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '13' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 794s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '16' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 794s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '19' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 794s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '21' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 794s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '22' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 794s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '23' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 794s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '25' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 794s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '27' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 794s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '30' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 794s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '33' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 794s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '36' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 794s 39 reads; of these: 794s 29 (74.36%) were paired; of these: 794s 29 (100.00%) aligned concordantly 0 times 794s 0 (0.00%) aligned concordantly exactly 1 time 794s 0 (0.00%) aligned concordantly >1 times 794s ---- 794s 29 pairs aligned concordantly 0 times; of these: 794s 0 (0.00%) aligned discordantly 1 time 794s ---- 794s 29 pairs aligned 0 times concordantly or discordantly; of these: 794s 58 mates make up the pairs; of these: 794s 53 (91.38%) aligned 0 times 794s 2 (3.45%) aligned exactly 1 time 794s 3 (5.17%) aligned >1 times 794s 10 (25.64%) were unpaired; of these: 794s 9 (90.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 1 (10.00%) aligned >1 times 794s 8.82% overall alignment rate 794s Read 50 alignments... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s AA 794s AA 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CG 794s CG 794s Processing line... 794s CG 794s CG 794s Processing line... 794s CG 794s CG 794s Processing line... 794s Processing line... 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s AT 794s AT 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s GACAACC 794s GACAACC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s AC 794s AC 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s CGAA 794s CGAA 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s Processing line... 794s --- Summary --- 794s Read 1 reference strings 794s Checked 27 alignments, 0 edits 794s --------------- 794s PASSED 794s ALSO checking that bowtie2 and bowtie2-align match up 794s /usr/bin/bowtie2 --cp-min 7 --large-index -R 2 --trim5 8 -i L,0.1209547034377,0.301705810076089 --cp-ival 1 -D 28 --nofw --mp 7.36994422247878,2.75023352670011 --trim3 7 --score-min L,1.37057882756889,6.72360711056115 --rdg 10.075879813847,2.38623908200782 --rfg 48.2699867803365 -a --mm -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 794s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 794s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '4' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 794s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '9' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 794s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '12' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 794s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '13' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 794s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '16' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 794s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '19' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 794s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '21' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 794s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '22' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 794s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '23' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 794s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '25' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 794s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '27' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 794s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '30' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 794s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 794s Warning: skipping mate #1 of read '33' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 794s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 794s Warning: skipping read '36' because it was < 2 characters long 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 794s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 794s 39 reads; of these: 794s 29 (74.36%) were paired; of these: 794s 29 (100.00%) aligned concordantly 0 times 794s 0 (0.00%) aligned concordantly exactly 1 time 794s 0 (0.00%) aligned concordantly >1 times 794s ---- 794s 29 pairs aligned concordantly 0 times; of these: 794s 0 (0.00%) aligned discordantly 1 time 794s ---- 794s 29 pairs aligned 0 times concordantly or discordantly; of these: 794s 58 mates make up the pairs; of these: 794s 53 (91.38%) aligned 0 times 794s 2 (3.45%) aligned exactly 1 time 794s 3 (5.17%) aligned >1 times 794s 10 (25.64%) were unpaired; of these: 794s 9 (90.00%) aligned 0 times 794s 0 (0.00%) aligned exactly 1 time 794s 1 (10.00%) aligned >1 times 794s 8.82% overall alignment rate 794s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 794s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 794s /usr/bin/bowtie2 --cp-min 7 --large-index -R 2 --trim5 8 -i L,0.1209547034377,0.301705810076089 --cp-ival 1 -D 28 --nofw --mp 7.36994422247878,2.75023352670011 --trim3 7 --score-min L,1.37057882756889,6.72360711056115 --rdg 10.075879813847,2.38623908200782 --rfg 48.2699867803365 -a --mm -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 795s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 795s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '4' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 795s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '9' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 795s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '12' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 795s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '13' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 795s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 795s Warning: skipping read '16' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 795s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '19' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 795s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '21' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 795s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 795s Warning: skipping read '22' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 795s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '23' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 795s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '25' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 795s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 795s Warning: skipping read '27' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 795s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '30' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 795s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '33' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 795s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 795s Warning: skipping read '36' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 795s 39 reads; of these: 795s 29 (74.36%) were paired; of these: 795s 29 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 29 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 29 pairs aligned 0 times concordantly or discordantly; of these: 795s 58 mates make up the pairs; of these: 795s 53 (91.38%) aligned 0 times 795s 2 (3.45%) aligned exactly 1 time 795s 3 (5.17%) aligned >1 times 795s 10 (25.64%) were unpaired; of these: 795s 9 (90.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 1 (10.00%) aligned >1 times 795s 8.82% overall alignment rate 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 795s Flattened IUPAC characters 795s Mutating sequence Sim.pm.1 795s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutating sequence Sim.pm.2 795s Introducing 2 SNPs, 1/1 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutated reference genome to subject genome 795s SNPs introduced: 9 795s Reference gaps introduced: 1 795s Read gaps introduced: 2 795s Rearrangements introduced: 0 795s Created read sampler 795s Sampling 100 reads 795s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 795s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 795s parsing sequence Sim.pm.1... 795s parsing sequence Sim.pm.2... 795s Parsed 78 reference bases 795s *** Run 3 of 100 795s /usr/bin/bowtie2 --cp-min 3 --large-index --trim5 0 --np 2 --nofw --cp-ival 1 --local --score-min L,9.82300606181636,6.53621777639655 --rdg 31.559731275112 --gbar 4 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 795s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 795s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 795s Read 50 alignments... 795s 100 reads; of these: 795s 100 (100.00%) were paired; of these: 795s 100 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 100 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 100 pairs aligned 0 times concordantly or discordantly; of these: 795s 200 mates make up the pairs; of these: 795s 200 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s Read 100 alignments... 795s Read 150 alignments... 795s Read 200 alignments... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing 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Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s --- Summary --- 795s Read 1 reference strings 795s Checked 0 alignments, 0 edits 795s --------------- 795s PASSED 795s ALSO checking that bowtie2 and bowtie2-align match up 795s /usr/bin/bowtie2 --cp-min 3 --large-index --trim5 0 --np 2 --nofw --cp-ival 1 --local --score-min L,9.82300606181636,6.53621777639655 --rdg 31.559731275112 --gbar 4 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 795s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 795s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 795s 100 reads; of these: 795s 100 (100.00%) were paired; of these: 795s 100 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 100 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 100 pairs aligned 0 times concordantly or discordantly; of these: 795s 200 mates make up the pairs; of these: 795s 200 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 795s /usr/bin/bowtie2 --cp-min 3 --large-index --trim5 0 --np 2 --nofw --cp-ival 1 --local --score-min L,9.82300606181636,6.53621777639655 --rdg 31.559731275112 --gbar 4 --qseq -p 3 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 795s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 795s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 795s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 795s 100 reads; of these: 795s 100 (100.00%) were paired; of these: 795s 100 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 100 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 100 pairs aligned 0 times concordantly or discordantly; of these: 795s 200 mates make up the pairs; of these: 795s 200 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 795s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 795s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 795s /usr/bin/bowtie2 --cp-min 3 --large-index --trim5 0 --np 2 --nofw --cp-ival 1 --local --score-min L,9.82300606181636,6.53621777639655 --rdg 31.559731275112 --gbar 4 --qseq -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 795s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 795s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 795s 100 reads; of these: 795s 100 (100.00%) were paired; of these: 795s 100 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 100 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 100 pairs aligned 0 times concordantly or discordantly; of these: 795s 200 mates make up the pairs; of these: 795s 200 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 795s Flattened IUPAC characters 795s Mutating sequence Sim.pm.1 795s Introducing 6 SNPs, 0/1 ref/read gaps, and 1 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutating sequence Sim.pm.2 795s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutated reference genome to subject genome 795s SNPs introduced: 7 795s Reference gaps introduced: 0 795s Read gaps introduced: 2 795s Rearrangements introduced: 1 795s Created read sampler 795s Sampling 89 reads 795s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 795s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 795s parsing sequence Sim.pm.1... 795s parsing sequence Sim.pm.2... 795s Parsed 78 reference bases 795s *** Run 4 of 100 795s /usr/bin/bowtie2 --large-index --cp-min 5 -k 3 --np 2 --mp 9.26618323271423,1.27514322865157 --cp-ival 2 --local --mm --score-min L,6.00840659286574,7.98251116485961 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 795s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '5' because it was < 2 characters long 795s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '8' because it was < 2 characters long 795s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '21' because it was < 2 characters long 795s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '28' because it was < 2 characters long 795s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '34' because it was < 2 characters long 795s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '52' because it was < 2 characters long 795s Read 50 alignments... 795s 89 reads; of these: 795s 89 (100.00%) were paired; of these: 795s 89 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 89 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 89 pairs aligned 0 times concordantly or discordantly; of these: 795s 178 mates make up the pairs; of these: 795s 178 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s Read 100 alignments... 795s Read 150 alignments... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s --- Summary --- 795s Read 1 reference strings 795s Checked 0 alignments, 0 edits 795s --------------- 795s PASSED 795s ALSO checking that bowtie2 and bowtie2-align match up 795s /usr/bin/bowtie2 --large-index --cp-min 5 -k 3 --np 2 --mp 9.26618323271423,1.27514322865157 --cp-ival 2 --local --mm --score-min L,6.00840659286574,7.98251116485961 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 795s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '5' because it was < 2 characters long 795s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '8' because it was < 2 characters long 795s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '21' because it was < 2 characters long 795s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '28' because it was < 2 characters long 795s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '34' because it was < 2 characters long 795s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '52' because it was < 2 characters long 795s 89 reads; of these: 795s 89 (100.00%) were paired; of these: 795s 89 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 89 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 89 pairs aligned 0 times concordantly or discordantly; of these: 795s 178 mates make up the pairs; of these: 795s 178 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 795s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 795s /usr/bin/bowtie2 --large-index --cp-min 5 -k 3 --np 2 --mp 9.26618323271423,1.27514322865157 --cp-ival 2 --local --mm --score-min L,6.00840659286574,7.98251116485961 -q -p 3 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 795s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '5' because it was < 2 characters long 795s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '8' because it was < 2 characters long 795s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '21' because it was < 2 characters long 795s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '28' because it was < 2 characters long 795s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '34' because it was < 2 characters long 795s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '52' because it was < 2 characters long 795s 89 reads; of these: 795s 89 (100.00%) were paired; of these: 795s 89 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 89 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 89 pairs aligned 0 times concordantly or discordantly; of these: 795s 178 mates make up the pairs; of these: 795s 178 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 795s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 795s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 795s /usr/bin/bowtie2 --large-index --cp-min 5 -k 3 --np 2 --mp 9.26618323271423,1.27514322865157 --cp-ival 2 --local --mm --score-min L,6.00840659286574,7.98251116485961 -q -p 3 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 795s Warning: skipping mate #2 of read '5' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '5' because it was < 2 characters long 795s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '8' because it was < 2 characters long 795s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '21' because it was < 2 characters long 795s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read '28' because it was < 2 characters long 795s Warning: skipping mate #2 of read '34' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '34' because it was < 2 characters long 795s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #2 of read '52' because it was < 2 characters long 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 795s *** Run 5 of 100 795s /usr/bin/bowtie2 --mm --rfg 43.1819349846172,2.77299201009065 --score-min L,2.95590690209162,8.68142522495293 --trim3 9 --local --cp-ival 1 --n-ceil 1.13885554126591,0.7814208152335 --np 1 --large-index --cp-min 2 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 795s *** Run 6 of 100 795s /usr/bin/bowtie2 -R 4 --cp-min 2 --large-index --mp 6.40344802676378,4.24307693944384 --cp-ival 1 --local -D 16 -a --score-min L,7.2210814234763,7.577283203634 --rfg 41.5526423039728,4.85152785823674 --gbar 1 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 795s 89 reads; of these: 795s 89 (100.00%) were paired; of these: 795s 89 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 89 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 89 pairs aligned 0 times concordantly or discordantly; of these: 795s 178 mates make up the pairs; of these: 795s 178 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s Flattened IUPAC characters 795s Mutating sequence Sim.pm.1 795s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutating sequence Sim.pm.2 795s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutated reference genome to subject genome 795s SNPs introduced: 10 795s Reference gaps introduced: 0 795s Read gaps introduced: 1 795s Rearrangements introduced: 0 795s Created read sampler 795s Sampling 85 reads 795s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 795s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 795s parsing sequence Sim.pm.1... 795s parsing sequence Sim.pm.2... 795s Parsed 78 reference bases 795s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 795s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 795s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 795s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 795s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 795s Read 50 alignments... 795s Read 100 alignments... 795s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 795s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 795s 85 reads; of these: 795s 67 (78.82%) were paired; of these: 795s 67 (100.00%) aligned concordantly 0 times 795s 0 (0.00%) aligned concordantly exactly 1 time 795s 0 (0.00%) aligned concordantly >1 times 795s ---- 795s 67 pairs aligned concordantly 0 times; of these: 795s 0 (0.00%) aligned discordantly 1 time 795s ---- 795s 67 pairs aligned 0 times concordantly or discordantly; of these: 795s 134 mates make up the pairs; of these: 795s 134 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 18 (21.18%) were unpaired; of these: 795s 18 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s Read 150 alignments... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s --- Summary --- 795s Read 1 reference strings 795s Checked 0 alignments, 0 edits 795s --------------- 795s PASSED 795s Flattened IUPAC characters 795s Mutating sequence Sim.pm.2 795s Introducing 8 SNPs, 1/0 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutating sequence Sim.pm.1 795s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutated reference genome to subject genome 795s SNPs introduced: 9 795s Reference gaps introduced: 1 795s Read gaps introduced: 1 795s Rearrangements introduced: 0 795s Created read sampler 795s Sampling 43 reads 795s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 795s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 795s parsing sequence Sim.pm.1... 795s parsing sequence Sim.pm.2... 795s Parsed 78 reference bases 795s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '4' because it was < 2 characters long 795s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '10' because it was < 2 characters long 795s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '36' because it was < 2 characters long 795s 43 reads; of these: 795s 43 (100.00%) were unpaired; of these: 795s 43 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s --- Summary --- 795s Read 1 reference strings 795s Checked 0 alignments, 0 edits 795s --------------- 795s PASSED 795s ALSO checking that bowtie2 and bowtie2-align match up 795s /usr/bin/bowtie2 -R 4 --cp-min 2 --large-index --mp 6.40344802676378,4.24307693944384 --cp-ival 1 --local -D 16 -a --score-min L,7.2210814234763,7.577283203634 --rfg 41.5526423039728,4.85152785823674 --gbar 1 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 795s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '4' because it was < 2 characters long 795s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '10' because it was < 2 characters long 795s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '36' because it was < 2 characters long 795s 43 reads; of these: 795s 43 (100.00%) were unpaired; of these: 795s 43 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 795s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 795s /usr/bin/bowtie2 -R 4 --cp-min 2 --large-index --mp 6.40344802676378,4.24307693944384 --cp-ival 1 --local -D 16 -a --score-min L,7.2210814234763,7.577283203634 --rfg 41.5526423039728,4.85152785823674 --gbar 1 -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 795s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '4' because it was < 2 characters long 795s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '10' because it was < 2 characters long 795s Warning: skipping read '36' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '36' because it was < 2 characters long 795s 43 reads; of these: 795s 43 (100.00%) were unpaired; of these: 795s 43 (100.00%) aligned 0 times 795s 0 (0.00%) aligned exactly 1 time 795s 0 (0.00%) aligned >1 times 795s 0.00% overall alignment rate 795s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 795s Flattened IUPAC characters 795s Mutating sequence Sim.pm.2 795s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutating sequence Sim.pm.1 795s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 795s Finished SNPs 795s Finished ref gaps 795s Finished read gaps 795s Mutated reference genome to subject genome 795s SNPs introduced: 7 795s Reference gaps introduced: 0 795s Read gaps introduced: 0 795s Rearrangements introduced: 0 795s Created read sampler 795s Sampling 49 reads 795s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 795s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 795s parsing sequence Sim.pm.1... 795s parsing sequence Sim.pm.2... 795s Parsed 78 reference bases 795s *** Run 7 of 100 795s /usr/bin/bowtie2 --large-index --cp-min 2 --ma 12.5945350404528 --np 1 -k 3 --trim5 1 --cp-ival 1 --n-ceil 0.389687536341809,1.18194013040742 --score-min L,8.0707546295664,4.86642307678515 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 795s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 795s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 795s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 795s Warning: skipping read '2' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 795s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '19' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 795s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 795s Warning: skipping read '34' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 795s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 795s Warning: skipping read '42' because it was < 2 characters long 795s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 795s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 795s 49 reads; of these: 795s 49 (100.00%) were unpaired; of these: 795s 40 (81.63%) aligned 0 times 795s 5 (10.20%) aligned exactly 1 time 795s 4 (8.16%) aligned >1 times 795s 18.37% overall alignment rate 795s Read 50 alignments... 795s Processing line... 795s Processing line... 795s Processing line... 795s /usr/bin/bowtie2 --large-index --cp-min 2 --ma 12.5945350404528 --np 1 -k 3 --trim5 1 --cp-ival 1 --n-ceil 0.389687536341809,1.18194013040742 --score-min L,8.0707546295664,4.86642307678515 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s ACAACTCATTG 795s ACAACTCATTG 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s TACCACAATATCACA 795s TACCACAATATCACA 795s Processing line... 795s ACCC 795s ACCC 795s Processing line... 795s CA 795s CA 795s Processing line... 795s CA 795s CA 795s Processing line... 795s CA 795s CA 795s Processing line... 795s Processing line... 795s CA 795s CA 795s Processing line... 795s CA 795s CA 795s Processing line... 795s CA 795s CA 795s Processing line... 795s Processing line... 795s Processing line... 795s TAATC 795s TAATC 795s Processing line... 795s AACCCG 795s AACCCG 795s Processing line... 795s Processing line... 795s Processing line... 795s CC 795s CC 795s Processing line... 795s CC 795s CC 795s Processing line... 795s CC 795s CC 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s CGA 795s CGA 795s Processing line... 795s TCG 795s TCG 795s Processing line... 795s TCG 795s TCG 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s Processing line... 795s --- Summary --- 795s Read 1 reference strings 795s Checked 17 alignments, 0 edits 795s --------------- 795s PASSED 795s ALSO checking that bowtie2 and bowtie2-align match up 796s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 796s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 796s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '2' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 796s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '19' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 796s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '34' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 796s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '42' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 796s 49 reads; of these: 796s 49 (100.00%) were unpaired; of these: 796s 40 (81.63%) aligned 0 times 796s 5 (10.20%) aligned exactly 1 time 796s 4 (8.16%) aligned >1 times 796s 18.37% overall alignment rate 796s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 796s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 796s /usr/bin/bowtie2 --large-index --cp-min 2 --ma 12.5945350404528 --np 1 -k 3 --trim5 1 --cp-ival 1 --n-ceil 0.389687536341809,1.18194013040742 --score-min L,8.0707546295664,4.86642307678515 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 796s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 796s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 796s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '2' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 796s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '19' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 796s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '34' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 796s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '42' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 796s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 796s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 796s 49 reads; of these: 796s 49 (100.00%) were unpaired; of these: 796s 40 (81.63%) aligned 0 times 796s 5 (10.20%) aligned exactly 1 time 796s 4 (8.16%) aligned >1 times 796s 18.37% overall alignment rate 796s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 796s Flattened IUPAC characters 796s Mutating sequence Sim.pm.2 796s Introducing 5 SNPs, 1/1 ref/read gaps, and 2 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutating sequence Sim.pm.1 796s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutated reference genome to subject genome 796s SNPs introduced: 8 796s Reference gaps introduced: 2 796s Read gaps introduced: 1 796s Rearrangements introduced: 2 796s Created read sampler 796s Sampling 101 reads 796s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 796s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 796s parsing sequence Sim.pm.1... 796s parsing sequence Sim.pm.2... 796s Parsed 78 reference bases 796s *** Run 8 of 100 796s /usr/bin/bowtie2 --cp-ival 4 --local --gbar 1 --score-min L,1.00066510404299,1.30545122360967 --rdg 10.5601928125212,17.1780775827992 -R 1 --cp-min 3 --large-index -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 796s Read 50 alignments... 796s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '67' because it was < 2 characters long 796s Warning: skipping mate #2 of read '78' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '78' because it was < 2 characters long 796s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '89' because it was < 2 characters long 796s Read 100 alignments... 796s 101 reads; of these: 796s 101 (100.00%) were paired; of these: 796s 100 (99.01%) aligned concordantly 0 times 796s 0 (0.00%) aligned concordantly exactly 1 time 796s 1 (0.99%) aligned concordantly >1 times 796s ---- 796s 100 pairs aligned concordantly 0 times; of these: 796s 1 (1.00%) aligned discordantly 1 time 796s ---- 796s 99 pairs aligned 0 times concordantly or discordantly; of these: 796s 198 mates make up the pairs; of these: 796s 179 (90.40%) aligned 0 times 796s 11 (5.56%) aligned exactly 1 time 796s 8 (4.04%) aligned >1 times 796s 11.39% overall alignment rate 796s Read 150 alignments... 796s Read 200 alignments... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GACAAC 796s GACAAC 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TAT 796s TAT 796s Processing line... 796s Processing line... 796s CACAT 796s CACAT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s ATCACAT 796s ATCACAT 796s Processing line... 796s Processing line... 796s CA 796s CA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TTC 796s TTC 796s Processing line... 796s Processing line... 796s TAC 796s TAC 796s Processing line... 796s Processing line... 796s TTG 796s TTG 796s Processing line... 796s Processing line... 796s GT 796s GT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GTCGTGGCAACCCGA 796s GTCGTGACAACCCGA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CAATATC 796s CAATATC 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s ATA 796s ATA 796s Processing line... 796s Processing line... 796s AC 796s AC 796s Processing line... 796s CAACCCGAACGTTAATCTTAC 796s CAACCCGAACNTTAATCNTAC 796s Processing line... 796s GG 796s GG 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CT 796s CT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TACCA 796s TACCA 796s Processing line... 796s CCC 796s CCC 796s Processing line... 796s Processing line... 796s Processing line... 796s ACAATATCA 796s ACAATATCA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TACCACAA 796s TACCACAA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CTG 796s CTG 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s ACAATAT 796s ACAATAT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s ACAT 796s ACAT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s --- Summary --- 796s Read 1 reference strings 796s Checked 23 alignments, 0 edits 796s --------------- 796s PASSED 796s ALSO checking that bowtie2 and bowtie2-align match up 796s /usr/bin/bowtie2 --cp-ival 4 --local --gbar 1 --score-min L,1.00066510404299,1.30545122360967 --rdg 10.5601928125212,17.1780775827992 -R 1 --cp-min 3 --large-index -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 796s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '67' because it was < 2 characters long 796s Warning: skipping mate #2 of read '78' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '78' because it was < 2 characters long 796s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '89' because it was < 2 characters long 796s 101 reads; of these: 796s 101 (100.00%) were paired; of these: 796s 100 (99.01%) aligned concordantly 0 times 796s 0 (0.00%) aligned concordantly exactly 1 time 796s 1 (0.99%) aligned concordantly >1 times 796s ---- 796s 100 pairs aligned concordantly 0 times; of these: 796s 1 (1.00%) aligned discordantly 1 time 796s ---- 796s 99 pairs aligned 0 times concordantly or discordantly; of these: 796s 198 mates make up the pairs; of these: 796s 179 (90.40%) aligned 0 times 796s 11 (5.56%) aligned exactly 1 time 796s 8 (4.04%) aligned >1 times 796s 11.39% overall alignment rate 796s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 796s /usr/bin/bowtie2 --cp-ival 4 --local --gbar 1 --score-min L,1.00066510404299,1.30545122360967 --rdg 10.5601928125212,17.1780775827992 -R 1 --cp-min 3 --large-index -r -p 3 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 796s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 796s Warning: skipping mate #1 of read '67' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '67' because it was < 2 characters long 796s Warning: skipping mate #2 of read '78' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '78' because it was < 2 characters long 796s Warning: skipping mate #2 of read '89' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '89' because it was < 2 characters long 796s 101 reads; of these: 796s 101 (100.00%) were paired; of these: 796s 100 (99.01%) aligned concordantly 0 times 796s 0 (0.00%) aligned concordantly exactly 1 time 796s 1 (0.99%) aligned concordantly >1 times 796s ---- 796s 100 pairs aligned concordantly 0 times; of these: 796s 1 (1.00%) aligned discordantly 1 time 796s ---- 796s 99 pairs aligned 0 times concordantly or discordantly; of these: 796s 198 mates make up the pairs; of these: 796s 179 (90.40%) aligned 0 times 796s 11 (5.56%) aligned exactly 1 time 796s 8 (4.04%) aligned >1 times 796s 11.39% overall alignment rate 796s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 796s Flattened IUPAC characters 796s Mutating sequence Sim.pm.2 796s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutating sequence Sim.pm.1 796s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutated reference genome to subject genome 796s SNPs introduced: 0 796s Reference gaps introduced: 0 796s Read gaps introduced: 0 796s Rearrangements introduced: 0 796s Created read sampler 796s Sampling 63 reads 796s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 796s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 796s parsing sequence Sim.pm.1... 796s parsing sequence Sim.pm.2... 796s Parsed 78 reference bases 796s *** Run 9 of 100 796s /usr/bin/bowtie2 --cp-min 7 --large-index --np 1 --cp-ival 1 -D 9 --n-ceil 1.02851418961012,0.645014467801075 --nofw --trim3 9 --score-min L,8.29521058085044,2.75885211839454 --rdg 8.3270080554279 --mm -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 796s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 796s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '2' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 796s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '4' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 796s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '6' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 796s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '7' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 796s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '8' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 796s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '10' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 796s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '15' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 796s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '16' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 796s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '17' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 796s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '18' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 796s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '21' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 796s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '23' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 796s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '24' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 796s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '28' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 796s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '31' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 796s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '40' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 796s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '47' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 796s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '48' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 796s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '49' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 796s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '50' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 796s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '52' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 796s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '53' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 796s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '56' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 796s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '57' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 796s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '58' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 796s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '60' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 796s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '61' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 796s 63 reads; of these: 796s 63 (100.00%) were unpaired; of these: 796s 57 (90.48%) aligned 0 times 796s 4 (6.35%) aligned exactly 1 time 796s 2 (3.17%) aligned >1 times 796s 9.52% overall alignment rate 796s /usr/bin/bowtie2 --cp-min 7 --large-index --np 1 --cp-ival 1 -D 9 --n-ceil 1.02851418961012,0.645014467801075 --nofw --trim3 9 --score-min L,8.29521058085044,2.75885211839454 --rdg 8.3270080554279 --mm -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 796s Read 50 alignments... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TCATT 796s TCATT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CGTGACA 796s CGTGACA 796s Processing line... 796s ATA 796s ATA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GA 796s GA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TCGTCGTGACA 796s TCGTCGTGACA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TACCA 796s TACCA 796s --- Summary --- 796s Read 1 reference strings 796s Checked 6 alignments, 0 edits 796s --------------- 796s PASSED 796s ALSO checking that bowtie2 and bowtie2-align match up 796s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 796s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '2' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 796s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '4' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 796s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '6' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 796s Warning: skipping read '7' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '7' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 796s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '8' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 796s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '10' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 796s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '15' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 796s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '16' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 796s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '17' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 796s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '18' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 796s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '21' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 796s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '23' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 796s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '24' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 796s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '28' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 796s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '31' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 796s Warning: skipping read '40' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '40' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 796s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '47' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 796s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '48' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 796s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '49' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 796s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '50' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 796s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '52' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 796s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '53' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 796s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '56' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 796s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '57' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 796s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '58' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 796s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '60' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 796s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '61' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 796s 63 reads; of these: 796s 63 (100.00%) were unpaired; of these: 796s 57 (90.48%) aligned 0 times 796s 4 (6.35%) aligned exactly 1 time 796s 2 (3.17%) aligned >1 times 796s 9.52% overall alignment rate 796s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 796s Flattened IUPAC characters 796s Mutating sequence Sim.pm.2 796s Introducing 10 SNPs, 0/0 ref/read gaps, and 2 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutating sequence Sim.pm.1 796s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutated reference genome to subject genome 796s SNPs introduced: 12 796s Reference gaps introduced: 0 796s Read gaps introduced: 0 796s Rearrangements introduced: 2 796s Created read sampler 796s Sampling 115 reads 796s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 796s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 796s parsing sequence Sim.pm.1... 796s parsing sequence Sim.pm.2... 796s Parsed 78 reference bases 796s *** Run 10 of 100 796s /usr/bin/bowtie2 -k 2 --large-index --cp-min 10 --gbar 1 --rdg 43.9633365612867 --score-min L,9.54557637142669,2.99228868416722 --mm --cp-ival 1 -N 1 -L16 --mp 6.40170867701305,1.42062069417572 --trim3 6 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 796s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 796s Warning: skipping read '4' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 796s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '18' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 796s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 796s Warning: skipping read '29' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 796s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (1) 796s Warning: skipping mate #2 of read '43' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 796s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '47' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 796s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '52' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 796s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '53' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 796s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '55' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 796s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '60' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 796s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '82' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 796s Warning: skipping read '85' because length (0) <= # seed mismatches (1) 796s Warning: skipping read '85' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 796s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '88' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 796s Warning: skipping mate #1 of read '89' because length (1) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '89' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 796s Warning: skipping mate #1 of read '93' because length (0) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '93' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 796s Warning: skipping mate #2 of read '105' because length (1) <= # seed mismatches (1) 796s Warning: skipping mate #2 of read '105' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 796s Warning: skipping mate #1 of read '110' because length (0) <= # seed mismatches (1) 796s Warning: skipping mate #1 of read '110' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 796s Warning: skipping read '114' because length (0) <= # seed mismatches (1) 796s Warning: skipping read '114' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 796s Warning: skipping mate #2 of read '115' because length (1) <= # seed mismatches (1) 796s Warning: skipping mate #2 of read '115' because it was < 2 characters long 796s Read 50 alignments... 796s Read 100 alignments... 796s 115 reads; of these: 796s 97 (84.35%) were paired; of these: 796s 97 (100.00%) aligned concordantly 0 times 796s 0 (0.00%) aligned concordantly exactly 1 time 796s 0 (0.00%) aligned concordantly >1 times 796s ---- 796s 97 pairs aligned concordantly 0 times; of these: 796s 0 (0.00%) aligned discordantly 1 time 796s ---- 796s 97 pairs aligned 0 times concordantly or discordantly; of these: 796s 194 mates make up the pairs; of these: 796s 183 (94.33%) aligned 0 times 796s 4 (2.06%) aligned exactly 1 time 796s 7 (3.61%) aligned >1 times 796s 18 (15.65%) were unpaired; of these: 796s 18 (100.00%) aligned 0 times 796s 0 (0.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 5.19% overall alignment rate 796s Read 150 alignments... 796s Read 200 alignments... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TTCG 796s TTCG 796s Processing line... 796s CGAA 796s CGAA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GT 796s GT 796s Processing line... 796s GT 796s GT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CAATAT 796s CAATAT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TTA 796s TTA 796s Processing line... 796s TAA 796s TAA 796s Processing line... 796s Processing line... 796s CC 796s CC 796s Processing line... 796s GG 796s GG 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CC 796s CC 796s Processing line... 796s CC 796s CC 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CC 796s CC 796s Processing line... 796s CC 796s CC 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CA 796s CA 796s Processing line... 796s CA 796s CA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CAACCC 796s CAACCC 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s TAC 796s TAC 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GAAC 796s GAAC 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s --- Summary --- 796s Read 1 reference strings 796s Checked 18 alignments, 0 edits 796s --------------- 796s PASSED 796s Flattened IUPAC characters 796s Mutating sequence Sim.pm.2 796s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutating sequence Sim.pm.1 796s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutated reference genome to subject genome 796s SNPs introduced: 10 796s Reference gaps introduced: 0 796s Read gaps introduced: 1 796s Rearrangements introduced: 1 796s Created read sampler 796s Sampling 67 reads 796s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 796s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 796s parsing sequence Sim.pm.1... 796s parsing sequence Sim.pm.2... 796s Parsed 78 reference bases 796s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 796s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 796s 67 reads; of these: 796s 67 (100.00%) were unpaired; of these: 796s 67 (100.00%) aligned 0 times 796s 0 (0.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 0.00% overall alignment rate 796s Read 50 alignments... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s --- Summary --- 796s Read 1 reference strings 796s Checked 0 alignments, 0 edits 796s --------------- 796s PASSED 796s Flattened IUPAC characters 796s Mutating sequence Sim.pm.1 796s Introducing 0 SNPs, 0/0 ref/read gaps, and 1 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutating sequence Sim.pm.2 796s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutated reference genome to subject genome 796s SNPs introduced: 5 796s Reference gaps introduced: 0 796s Read gaps introduced: 1 796s Rearrangements introduced: 1 796s Created read sampler 796s Sampling 71 reads 796s *** Run 11 of 100 796s /usr/bin/bowtie2 --cp-ival 2 --local -D 12 --rfg 25.4094071368685 --rdg 9.45468833467388 --score-min L,2.77323061168408,6.12545690809555 --gbar 2 --mm --large-index --cp-min 5 --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 796s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 796s *** Run 12 of 100 796s /usr/bin/bowtie2 --large-index --cp-min 2 --ma 20.1259306481593 --np 3 --norc --cp-ival 1 --rfg 42.2433957195322 --rdg 1.26629363914717,15.7658230150561 --score-min L,1.99195006690722,5.09507953519084 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 796s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 796s parsing sequence Sim.pm.1... 796s parsing sequence Sim.pm.2... 796s Parsed 78 reference bases 796s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 796s Warning: skipping mate #2 of read '2' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '2' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 796s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '15' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 796s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '22' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 796s Warning: skipping mate #2 of read '23' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #2 of read '23' because it was < 2 characters long 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 796s Read 50 alignments... 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 796s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 796s Read 100 alignments... 796s 71 reads; of these: 796s 71 (100.00%) were paired; of these: 796s 71 (100.00%) aligned concordantly 0 times 796s 0 (0.00%) aligned concordantly exactly 1 time 796s 0 (0.00%) aligned concordantly >1 times 796s ---- 796s 71 pairs aligned concordantly 0 times; of these: 796s 0 (0.00%) aligned discordantly 1 time 796s ---- 796s 71 pairs aligned 0 times concordantly or discordantly; of these: 796s 142 mates make up the pairs; of these: 796s 136 (95.77%) aligned 0 times 796s 2 (1.41%) aligned exactly 1 time 796s 4 (2.82%) aligned >1 times 796s 4.23% overall alignment rate 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GA 796s GA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GAC 796s GAC 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GA 796s GA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s CA 796s CA 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s AATAT 796s AATAT 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s GTC 796s GTC 796s Processing line... 796s Processing line... 796s Processing line... 796s --- Summary --- 796s Read 1 reference strings 796s Checked 6 alignments, 0 edits 796s --------------- 796s PASSED 796s Flattened IUPAC characters 796s Mutating sequence Sim.pm.1 796s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutating sequence Sim.pm.2 796s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutated reference genome to subject genome 796s SNPs introduced: 5 796s Reference gaps introduced: 0 796s Read gaps introduced: 1 796s Rearrangements introduced: 0 796s Created read sampler 796s Sampling 231 reads 796s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 796s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 796s parsing sequence Sim.pm.1... 796s parsing sequence Sim.pm.2... 796s Parsed 78 reference bases 796s *** Run 13 of 100 796s /usr/bin/bowtie2 --large-index --cp-min 3 --np 2 -i L,0.0188182788433292,2.941569124364 --nofw --local --cp-ival 1 --trim3 0 --rfg 26.0577465807593 --score-min L,7.38082818285115,3.61168947629333 --mm -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 796s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '111' because it was < 2 characters long 796s Warning: skipping read '119' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '119' because it was < 2 characters long 796s Warning: skipping read '189' because length (1) <= # seed mismatches (0) 796s Read 50 alignments... 796s Read 100 alignments... 796s Read 150 alignments... 796s Warning: skipping read '189' because it was < 2 characters long 796s 231 reads; of these: 796s 231 (100.00%) were unpaired; of these: 796s 231 (100.00%) aligned 0 times 796s 0 (0.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 0.00% overall alignment rate 796s Read 200 alignments... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s /usr/bin/bowtie2 --large-index --cp-min 3 --np 2 -i L,0.0188182788433292,2.941569124364 --nofw --local --cp-ival 1 --trim3 0 --rfg 26.0577465807593 --score-min L,7.38082818285115,3.61168947629333 --mm -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s --- Summary --- 796s Read 1 reference strings 796s Checked 0 alignments, 0 edits 796s --------------- 796s PASSED 796s ALSO checking that bowtie2 and bowtie2-align match up 796s Warning: skipping read '111' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '111' because it was < 2 characters long 796s Warning: skipping read '119' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '119' because it was < 2 characters long 796s Warning: skipping read '189' because length (1) <= # seed mismatches (0) 796s Warning: skipping read '189' because it was < 2 characters long 796s 231 reads; of these: 796s 231 (100.00%) were unpaired; of these: 796s 231 (100.00%) aligned 0 times 796s 0 (0.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 0.00% overall alignment rate 796s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 796s Flattened IUPAC characters 796s Mutating sequence Sim.pm.1 796s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutating sequence Sim.pm.2 796s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutated reference genome to subject genome 796s SNPs introduced: 8 796s Reference gaps introduced: 0 796s Read gaps introduced: 1 796s Rearrangements introduced: 0 796s Created read sampler 796s Sampling 65 reads 796s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 796s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 796s parsing sequence Sim.pm.1... 796s parsing sequence Sim.pm.2... 796s Parsed 78 reference bases 796s *** Run 14 of 100 796s /usr/bin/bowtie2 -R 2 --large-index --cp-min 2 --trim5 4 --norc --trim3 4 --local --cp-ival 1 --mm --gbar 3 --rfg 26.6148757567929,14.4981822745621 --rdg 16.2113547050232 --score-min L,8.18208962654584,2.95041701094501 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 796s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '3' because it was < 2 characters long 796s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '10' because it was < 2 characters long 796s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '21' because it was < 2 characters long 796s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '24' because it was < 2 characters long 796s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '30' because it was < 2 characters long 796s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '38' because it was < 2 characters long 796s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '43' because it was < 2 characters long 796s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '45' because it was < 2 characters long 796s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '46' because it was < 2 characters long 796s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '48' because it was < 2 characters long 796s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '62' because it was < 2 characters long 796s Read 50 alignments... 796s Read 100 alignments... 796s 65 reads; of these: 796s 56 (86.15%) were paired; of these: 796s 56 (100.00%) aligned concordantly 0 times 796s 0 (0.00%) aligned concordantly exactly 1 time 796s 0 (0.00%) aligned concordantly >1 times 796s ---- 796s 56 pairs aligned concordantly 0 times; of these: 796s 0 (0.00%) aligned discordantly 1 time 796s ---- 796s 56 pairs aligned 0 times concordantly or discordantly; of these: 796s 112 mates make up the pairs; of these: 796s 112 (100.00%) aligned 0 times 796s 0 (0.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 9 (13.85%) were unpaired; of these: 796s 9 (100.00%) aligned 0 times 796s 0 (0.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 0.00% overall alignment rate 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s /usr/bin/bowtie2 -R 2 --large-index --cp-min 2 --trim5 4 --norc --trim3 4 --local --cp-ival 1 --mm --gbar 3 --rfg 26.6148757567929,14.4981822745621 --rdg 16.2113547050232 --score-min L,8.18208962654584,2.95041701094501 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s Processing line... 796s --- Summary --- 796s Read 1 reference strings 796s Checked 0 alignments, 0 edits 796s --------------- 796s PASSED 796s ALSO checking that bowtie2 and bowtie2-align match up 796s Warning: skipping mate #1 of read '3' because length (1) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '3' because it was < 2 characters long 796s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '10' because it was < 2 characters long 796s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '21' because it was < 2 characters long 796s Warning: skipping mate #1 of read '24' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '24' because it was < 2 characters long 796s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 796s Warning: skipping read '30' because it was < 2 characters long 796s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '38' because it was < 2 characters long 796s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '43' because it was < 2 characters long 796s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '45' because it was < 2 characters long 796s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '46' because it was < 2 characters long 796s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '48' because it was < 2 characters long 796s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 796s Warning: skipping mate #1 of read '62' because it was < 2 characters long 796s 65 reads; of these: 796s 56 (86.15%) were paired; of these: 796s 56 (100.00%) aligned concordantly 0 times 796s 0 (0.00%) aligned concordantly exactly 1 time 796s 0 (0.00%) aligned concordantly >1 times 796s ---- 796s 56 pairs aligned concordantly 0 times; of these: 796s 0 (0.00%) aligned discordantly 1 time 796s ---- 796s 56 pairs aligned 0 times concordantly or discordantly; of these: 796s 112 mates make up the pairs; of these: 796s 112 (100.00%) aligned 0 times 796s 0 (0.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 9 (13.85%) were unpaired; of these: 796s 9 (100.00%) aligned 0 times 796s 0 (0.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 0.00% overall alignment rate 796s Flattened IUPAC characters 796s Mutating sequence Sim.pm.1 796s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutating sequence Sim.pm.2 796s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 796s Finished SNPs 796s Finished ref gaps 796s Finished read gaps 796s Mutated reference genome to subject genome 796s SNPs introduced: 6 796s Reference gaps introduced: 0 796s Read gaps introduced: 1 796s Rearrangements introduced: 2 796s Created read sampler 796s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 796s Sampling 113 reads 796s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 796s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 796s parsing sequence Sim.pm.1... 796s parsing sequence Sim.pm.2... 796s Parsed 78 reference bases 796s *** Run 15 of 100 796s /usr/bin/bowtie2 --score-min L,7.43342639172508,4.84110508043968 --rdg 25.584713297291 --cp-ival 1 -D 22 -N 0 -L27 --np 2 --trim5 6 --cp-min 2 --large-index --ma 15.1131014389049 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 797s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 797s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 797s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '6' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 797s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '9' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 797s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '10' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 797s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '13' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 797s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '16' because it was < 2 characters long 797s Warning: skipping mate #2 of read '16' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 797s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '39' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 797s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '40' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 797s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '41' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 797s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '56' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 797s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '57' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 797s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #2 of read '61' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 797s Read 50 alignments... 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 797s Warning: skipping mate #1 of read '69' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '69' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 797s Warning: skipping mate #1 of read '75' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '75' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 797s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '78' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 797s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '81' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 797s Warning: skipping mate #1 of read '85' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '85' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 797s Warning: skipping mate #2 of read '87' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #2 of read '87' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 797s Read 100 alignments... 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 797s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '96' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 797s Warning: skipping mate #1 of read '103' because length (0) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '103' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 797s 113 reads; of these: 797s 103 (91.15%) were paired; of these: 797s 102 (99.03%) aligned concordantly 0 times 797s 1 (0.97%) aligned concordantly exactly 1 time 797s 0 (0.00%) aligned concordantly >1 times 797s ---- 797s 102 pairs aligned concordantly 0 times; of these: 797s 0 (0.00%) aligned discordantly 1 time 797s ---- 797s 102 pairs aligned 0 times concordantly or discordantly; of these: 797s 204 mates make up the pairs; of these: 797s 189 (92.65%) aligned 0 times 797s 5 (2.45%) aligned exactly 1 time 797s 10 (4.90%) aligned >1 times 797s 10 (8.85%) were unpaired; of these: 797s 9 (90.00%) aligned 0 times 797s 1 (10.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 8.33% overall alignment rate 797s Read 150 alignments... 797s Read 200 alignments... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s CCACAAT 797s CCACAAT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s AT 797s AT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s TCACA 797s TCACA 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s ATC 797s ATC 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s AA 797s AA 797s Processing line... 797s Processing line... 797s GTCGTG 797s GTCGTG 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s GG 797s GG 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s CCA 797s CCA 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s TG 797s TG 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s ATCAC 797s ATCAC 797s *** Run 16 of 100 797s /usr/bin/bowtie2 --rfg 10.7844556298474 --score-min L,9.51990772233911,8.13046607379318 --mm --cp-ival 1 --nofw --norc -i S,1.19170606569155 --large-index --cp-min 6 --ma 35.9982976149094 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s CAATAT 797s CAATAT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s AAT 797s AAT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s GTCGTGACAACCCGA 797s GTCGTGACAACCCGA 797s Processing line... 797s TT 797s TT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s ACCACAATATCACA 797s ACCACAATATCACA 797s Processing line... 797s ATATCACAT 797s ATATCACAT 797s Processing line... 797s Processing line... 797s Processing line... 797s CC 797s CC 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s ACAAC 797s ACAAC 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s --- Summary --- 797s Read 1 reference strings 797s Checked 18 alignments, 0 edits 797s --------------- 797s PASSED 797s Flattened IUPAC characters 797s Mutating sequence Sim.pm.2 797s Introducing 4 SNPs, 0/1 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutating sequence Sim.pm.1 797s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutated reference genome to subject genome 797s SNPs introduced: 4 797s Reference gaps introduced: 0 797s Read gaps introduced: 1 797s Rearrangements introduced: 0 797s Created read sampler 797s Sampling 96 reads 797s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 797s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 797s parsing sequence Sim.pm.1... 797s parsing sequence Sim.pm.2... 797s Parsed 78 reference bases 797s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 797s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '39' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 797s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '45' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 797s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '47' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 797s Read 50 alignments... 797s 96 reads; of these: 797s 96 (100.00%) were paired; of these: 797s 96 (100.00%) aligned concordantly 0 times 797s 0 (0.00%) aligned concordantly exactly 1 time 797s 0 (0.00%) aligned concordantly >1 times 797s ---- 797s 96 pairs aligned concordantly 0 times; of these: 797s 0 (0.00%) aligned discordantly 1 time 797s ---- 797s 96 pairs aligned 0 times concordantly or discordantly; of these: 797s 192 mates make up the pairs; of these: 797s 192 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s Read 100 alignments... 797s Read 150 alignments... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s --- Summary --- 797s Read 1 reference strings 797s Checked 0 alignments, 0 edits 797s --------------- 797s PASSED 797s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 797s /usr/bin/bowtie2 --rfg 10.7844556298474 --score-min L,9.51990772233911,8.13046607379318 --mm --cp-ival 1 --nofw --norc -i S,1.19170606569155 --large-index --cp-min 6 --ma 35.9982976149094 -r -p 3 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 797s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 797s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '39' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 797s Warning: skipping mate #1 of read '45' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '45' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 797s Warning: skipping mate #1 of read '47' because length (1) <= # seed mismatches (0) 797s Warning: skipping mate #1 of read '47' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 797s 96 reads; of these: 797s 96 (100.00%) were paired; of these: 797s 96 (100.00%) aligned concordantly 0 times 797s 0 (0.00%) aligned concordantly exactly 1 time 797s 0 (0.00%) aligned concordantly >1 times 797s ---- 797s 96 pairs aligned concordantly 0 times; of these: 797s 0 (0.00%) aligned discordantly 1 time 797s ---- 797s 96 pairs aligned 0 times concordantly or discordantly; of these: 797s 192 mates make up the pairs; of these: 797s 192 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 797s Flattened IUPAC characters 797s Mutating sequence Sim.pm.2 797s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutating sequence Sim.pm.1 797s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutated reference genome to subject genome 797s SNPs introduced: 9 797s Reference gaps introduced: 0 797s Read gaps introduced: 0 797s Rearrangements introduced: 0 797s Created read sampler 797s Sampling 93 reads 797s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 797s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 797s parsing sequence Sim.pm.1... 797s parsing sequence Sim.pm.2... 797s Parsed 78 reference bases 797s *** Run 17 of 100 797s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --large-index -M 9 --mm --score-min L,5.61852838638002,7.48612331427656 --np 8 -r -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw 797s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 797s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 797s 93 reads; of these: 797s 93 (100.00%) were unpaired; of these: 797s 81 (87.10%) aligned 0 times 797s 6 (6.45%) aligned exactly 1 time 797s 6 (6.45%) aligned >1 times 797s 12.90% overall alignment rate 797s Read 50 alignments... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s AATATC 797s AATATC 797s Processing line... 797s TTGGAA 797s TTGGAA 797s Processing line... 797s ACAACCCGA 797s ACAACCCGA 797s Processing line... 797s Processing line... 797s TC 797s TC 797s Processing line... 797s CG 797s CG 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s AT 797s AT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s TCATTGGAATA 797s TCATTGGAATA 797s Processing line... 797s CAT 797s CAT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s AAT 797s AAT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s ATCAC 797s ATCAC 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s TAC 797s TAC 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s CA 797s CA 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s --- Summary --- 797s Read 1 reference strings 797s Checked 12 alignments, 0 edits 797s --------------- 797s PASSED 797s ALSO checking that bowtie2 and bowtie2-align match up 797s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --large-index -M 9 --mm --score-min L,5.61852838638002,7.48612331427656 --np 8 -r -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 797s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 797s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 797s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --large-index -M 9 --mm --score-min L,5.61852838638002,7.48612331427656 --np 8 -r -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 797s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 797s 93 reads; of these: 797s 93 (100.00%) were unpaired; of these: 797s 81 (87.10%) aligned 0 times 797s 6 (6.45%) aligned exactly 1 time 797s 6 (6.45%) aligned >1 times 797s 12.90% overall alignment rate 797s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 797s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 797s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 797s 93 reads; of these: 797s 93 (100.00%) were unpaired; of these: 797s 81 (87.10%) aligned 0 times 797s 6 (6.45%) aligned exactly 1 time 797s 6 (6.45%) aligned >1 times 797s 12.90% overall alignment rate 797s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 797s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 797s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 797s /usr/bin/bowtie2 --cp-min 2 --cp-ival 1 --large-index -M 9 --mm --score-min L,5.61852838638002,7.48612331427656 --np 8 -r -p 3 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 797s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 797s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 797s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 797s 93 reads; of these: 797s 93 (100.00%) were unpaired; of these: 797s 81 (87.10%) aligned 0 times 797s 6 (6.45%) aligned exactly 1 time 797s 6 (6.45%) aligned >1 times 797s 12.90% overall alignment rate 797s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 797s Flattened IUPAC characters 797s Mutating sequence Sim.pm.1 797s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutating sequence Sim.pm.2 797s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutated reference genome to subject genome 797s SNPs introduced: 6 797s Reference gaps introduced: 0 797s Read gaps introduced: 0 797s Rearrangements introduced: 0 797s Created read sampler 797s Sampling 99 reads 797s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 797s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 797s parsing sequence Sim.pm.1... 797s parsing sequence Sim.pm.2... 797s Parsed 78 reference bases 797s *** Run 18 of 100 797s /usr/bin/bowtie2 --mm --score-min L,4.48810325120053,2.32521253435084 --rdg 19.9652970079567 --mp 7.51475309289713,3.01546442942437 --n-ceil 1.2601859958916,0.465239732547373 --cp-ival 1 -k 2 --norc --np 7 --cp-min 3 --large-index -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 797s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 797s Warning: skipping read '9' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '9' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 797s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '20' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 797s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '22' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 797s Warning: skipping read '34' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '34' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 797s Warning: skipping read '39' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '39' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 797s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '42' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 797s Warning: skipping read '49' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '49' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 797s Warning: skipping read '83' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '83' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 797s Warning: skipping read '85' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '85' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 797s Warning: skipping read '97' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '97' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 797s Warning: skipping read '98' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '98' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 797s 99 reads; of these: 797s 99 (100.00%) were unpaired; of these: 797s 86 (86.87%) aligned 0 times 797s 4 (4.04%) aligned exactly 1 time 797s 9 (9.09%) aligned >1 times 797s 13.13% overall alignment rate 797s Read 50 alignments... 797s Read 100 alignments... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s TGGA 797s TGGA 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s TGTC 797s TGTC 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s CAT 797s CAT 797s Processing line... 797s CAT 797s CAT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s ACA 797s ACA 797s Processing line... 797s ACA 797s ACA 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s *** Run 19 of 100 797s /usr/bin/bowtie2 --cp-ival 2 --mp 9.65333968844911,6.32642335851956 --trim3 8 --score-min L,7.80041051005707,5.27858612438656 --rdg 3.49288517045567,2.84358765869632 --cp-min 3 --large-index --norc -k 3 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 797s Processing line... 797s Processing line... 797s Processing line... 797s GTG 797s GTG 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s AA 797s AA 797s Processing line... 797s AA 797s AA 797s Processing line... 797s Processing line... 797s CC 797s CC 797s Processing line... 797s CC 797s CC 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s GG 797s GG 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s ACAAC 797s ACAAC 797s Processing line... 797s ACAAC 797s ACAAC 797s Processing line... 797s Processing line... 797s AT 797s AT 797s Processing line... 797s AT 797s AT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s CT 797s CT 797s Processing line... 797s CT 797s CT 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s AA 797s AA 797s Processing line... 797s AA 797s AA 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s CA 797s CA 797s Processing line... 797s CA 797s CA 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s --- Summary --- 797s Read 1 reference strings 797s Checked 22 alignments, 0 edits 797s --------------- 797s PASSED 797s Flattened IUPAC characters 797s Mutating sequence Sim.pm.2 797s Introducing 7 SNPs, 0/1 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutating sequence Sim.pm.1 797s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutated reference genome to subject genome 797s SNPs introduced: 13 797s Reference gaps introduced: 1 797s Read gaps introduced: 1 797s Rearrangements introduced: 0 797s Created read sampler 797s Sampling 24 reads 797s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 797s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 797s parsing sequence Sim.pm.1... 797s parsing sequence Sim.pm.2... 797s Parsed 78 reference bases 797s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 797s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '1' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 797s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '2' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 797s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '9' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 797s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '11' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 797s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '13' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 797s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '15' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 797s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '18' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 797s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '20' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 797s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '23' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 797s 24 reads; of these: 797s 24 (100.00%) were unpaired; of these: 797s 24 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s --- Summary --- 797s Read 1 reference strings 797s Checked 0 alignments, 0 edits 797s --------------- 797s PASSED 797s ALSO checking that bowtie2 and bowtie2-align match up 797s /usr/bin/bowtie2 --cp-ival 2 --mp 9.65333968844911,6.32642335851956 --trim3 8 --score-min L,7.80041051005707,5.27858612438656 --rdg 3.49288517045567,2.84358765869632 --cp-min 3 --large-index --norc -k 3 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 797s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 797s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '1' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 797s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '2' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 797s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '9' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 797s Warning: skipping read '11' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '11' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 797s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '13' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 797s Warning: skipping read '15' because length (1) <= # seed mismatches (0) 797s Warning: skipping read '15' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 797s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '18' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 797s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '20' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 797s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 797s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 797s Warning: skipping read '23' because it was < 2 characters long 797s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 797s 24 reads; of these: 797s 24 (100.00%) were unpaired; of these: 797s 24 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 797s Flattened IUPAC characters 797s Mutating sequence Sim.pm.2 797s Introducing 2 SNPs, 0/2 ref/read gaps, and 1 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutating sequence Sim.pm.1 797s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutated reference genome to subject genome 797s SNPs introduced: 3 797s Reference gaps introduced: 1 797s Read gaps introduced: 2 797s Rearrangements introduced: 1 797s Created read sampler 797s Sampling 16 reads 797s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 797s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 797s parsing sequence Sim.pm.1... 797s parsing sequence Sim.pm.2... 797s Parsed 78 reference bases 797s *** Run 20 of 100 797s /usr/bin/bowtie2 -M 2 --trim5 4 --np 1 --cp-min 3 --large-index --score-min L,1.60588282695973,4.28455573189409 --rfg 21.0274658051015,13.2071411496061 --trim3 0 --nofw -N 1 -L16 --mp 8.15610661416737,2.0341272186026 --cp-ival 1 --local -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 797s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 797s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '1' because it was < 2 characters long 797s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '3' because it was < 2 characters long 797s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '7' because it was < 2 characters long 797s Warning: skipping read '12' because length (1) <= # seed mismatches (1) 797s Warning: skipping read '12' because it was < 2 characters long 797s 16 reads; of these: 797s 16 (100.00%) were unpaired; of these: 797s 16 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s --- Summary --- 797s Read 1 reference strings 797s Checked 0 alignments, 0 edits 797s --------------- 797s PASSED 797s ALSO checking that bowtie2 and bowtie2-align match up 797s /usr/bin/bowtie2 -M 2 --trim5 4 --np 1 --cp-min 3 --large-index --score-min L,1.60588282695973,4.28455573189409 --rfg 21.0274658051015,13.2071411496061 --trim3 0 --nofw -N 1 -L16 --mp 8.15610661416737,2.0341272186026 --cp-ival 1 --local -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 797s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 797s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '1' because it was < 2 characters long 797s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '3' because it was < 2 characters long 797s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '7' because it was < 2 characters long 797s Warning: skipping read '12' because length (1) <= # seed mismatches (1) 797s Warning: skipping read '12' because it was < 2 characters long 797s 16 reads; of these: 797s 16 (100.00%) were unpaired; of these: 797s 16 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 797s /usr/bin/bowtie2 -M 2 --trim5 4 --np 1 --cp-min 3 --large-index --score-min L,1.60588282695973,4.28455573189409 --rfg 21.0274658051015,13.2071411496061 --trim3 0 --nofw -N 1 -L16 --mp 8.15610661416737,2.0341272186026 --cp-ival 1 --local -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 797s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 797s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 797s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '1' because it was < 2 characters long 797s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '3' because it was < 2 characters long 797s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '7' because it was < 2 characters long 797s Warning: skipping read '12' because length (1) <= # seed mismatches (1) 797s Warning: skipping read '12' because it was < 2 characters long 797s 16 reads; of these: 797s 16 (100.00%) were unpaired; of these: 797s 16 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 797s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 797s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 797s /usr/bin/bowtie2 -M 2 --trim5 4 --np 1 --cp-min 3 --large-index --score-min L,1.60588282695973,4.28455573189409 --rfg 21.0274658051015,13.2071411496061 --trim3 0 --nofw -N 1 -L16 --mp 8.15610661416737,2.0341272186026 --cp-ival 1 --local -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 797s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 797s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 797s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '1' because it was < 2 characters long 797s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '3' because it was < 2 characters long 797s Warning: skipping read '7' because length (0) <= # seed mismatches (1) 797s Warning: skipping read '7' because it was < 2 characters long 797s Warning: skipping read '12' because length (1) <= # seed mismatches (1) 797s Warning: skipping read '12' because it was < 2 characters long 797s 16 reads; of these: 797s 16 (100.00%) were unpaired; of these: 797s 16 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 797s Flattened IUPAC characters 797s Mutating sequence Sim.pm.2 797s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutating sequence Sim.pm.1 797s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 797s Finished SNPs 797s Finished ref gaps 797s Finished read gaps 797s Mutated reference genome to subject genome 797s SNPs introduced: 7 797s Reference gaps introduced: 0 797s Read gaps introduced: 1 797s Rearrangements introduced: 0 797s Created read sampler 797s Sampling 85 reads 797s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 797s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 797s parsing sequence Sim.pm.1... 797s parsing sequence Sim.pm.2... 797s Parsed 78 reference bases 797s *** Run 21 of 100 797s /usr/bin/bowtie2 --cp-min 14 --large-index --norc --np 5 --trim5 0 --nofw --mp 8.30726885009457,3.03430489074249 --local --cp-ival 1 --score-min L,2.06402863256747,1.23518934752377 --rfg 19.6048340030997,18.3025790842805 --rdg 34.1687615040432 --mm -a --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 797s 85 reads; of these: 797s 85 (100.00%) were unpaired; of these: 797s 85 (100.00%) aligned 0 times 797s 0 (0.00%) aligned exactly 1 time 797s 0 (0.00%) aligned >1 times 797s 0.00% overall alignment rate 797s Read 50 alignments... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s Processing line... 797s --- Summary --- 797s Read 1 reference strings 797s Checked 0 alignments, 0 edits 797s --------------- 797s PASSED 797s ALSO checking that bowtie2 and bowtie2-align match up 797s /usr/bin/bowtie2 --cp-min 14 --large-index --norc --np 5 --trim5 0 --nofw --mp 8.30726885009457,3.03430489074249 --local --cp-ival 1 --score-min L,2.06402863256747,1.23518934752377 --rfg 19.6048340030997,18.3025790842805 --rdg 34.1687615040432 --mm -a --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 798s 85 reads; of these: 798s 85 (100.00%) were unpaired; of these: 798s 85 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 0.00% overall alignment rate 798s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 798s /usr/bin/bowtie2 --cp-min 14 --large-index --norc --np 5 --trim5 0 --nofw --mp 8.30726885009457,3.03430489074249 --local --cp-ival 1 --score-min L,2.06402863256747,1.23518934752377 --rfg 19.6048340030997,18.3025790842805 --rdg 34.1687615040432 --mm -a --qseq -p 3 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 798s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 798s 85 reads; of these: 798s 85 (100.00%) were unpaired; of these: 798s 85 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 0.00% overall alignment rate 798s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 798s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 798s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.2 798s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.1 798s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 6 798s Reference gaps introduced: 0 798s Read gaps introduced: 0 798s Rearrangements introduced: 1 798s Created read sampler 798s Sampling 37 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s *** Run 22 of 100 798s /usr/bin/bowtie2 --np 1 --cp-min 9 --large-index --mm --score-min L,5.32237347746349,2.89049109476234 --rfg 46.9866642425146 --local --cp-ival 1 -D 30 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 798s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '21' because it was < 2 characters long 798s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '24' because it was < 2 characters long 798s 37 reads; of these: 798s 37 (100.00%) were paired; of these: 798s 37 (100.00%) aligned concordantly 0 times 798s 0 (0.00%) aligned concordantly exactly 1 time 798s 0 (0.00%) aligned concordantly >1 times 798s ---- 798s 37 pairs aligned concordantly 0 times; of these: 798s 0 (0.00%) aligned discordantly 1 time 798s ---- 798s 37 pairs aligned 0 times concordantly or discordantly; of these: 798s 74 mates make up the pairs; of these: 798s 74 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 0.00% overall alignment rate 798s Read 50 alignments... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 0 alignments, 0 edits 798s --------------- 798s PASSED 798s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 798s /usr/bin/bowtie2 --np 1 --cp-min 9 --large-index --mm --score-min L,5.32237347746349,2.89049109476234 --rfg 46.9866642425146 --local --cp-ival 1 -D 30 -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 798s Warning: skipping mate #1 of read '21' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '21' because it was < 2 characters long 798s Warning: skipping mate #1 of read '24' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '24' because it was < 2 characters long 798s 37 reads; of these: 798s 37 (100.00%) were paired; of these: 798s 37 (100.00%) aligned concordantly 0 times 798s 0 (0.00%) aligned concordantly exactly 1 time 798s 0 (0.00%) aligned concordantly >1 times 798s ---- 798s 37 pairs aligned concordantly 0 times; of these: 798s 0 (0.00%) aligned discordantly 1 time 798s ---- 798s 37 pairs aligned 0 times concordantly or discordantly; of these: 798s 74 mates make up the pairs; of these: 798s 74 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 0.00% overall alignment rate 798s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 798s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 798s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.1 798s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.2 798s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 2 798s Reference gaps introduced: 0 798s Read gaps introduced: 1 798s Rearrangements introduced: 0 798s Created read sampler 798s Sampling 166 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s *** Run 23 of 100 798s /usr/bin/bowtie2 --cp-ival 3 --large-index --cp-min 3 --mp 9.95387422157419,5.89848864468352 -i C,0.554443547561626 --trim5 3 -M 6 --mm --score-min L,2.75052339387801,5.89226526154324 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 798s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 798s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 798s Warning: skipping read '19' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '19' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 798s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '44' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 798s Warning: skipping read '45' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '45' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 798s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '56' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 798s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '63' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 798s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '64' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 798s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '70' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 798s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '84' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 798s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '99' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 798s Warning: skipping read '126' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '126' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 798s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '130' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '146; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '147; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '148; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '149; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '150; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '151; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '152; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '153; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '154; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '155; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '156; setting to 0 instead 798s Warning: skipping read '156' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '156' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '157; setting to 0 instead 798s Warning: skipping read '157' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '157' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '158; setting to 0 instead 798s Warning: skipping read '158' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '158' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '159; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '160; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '161; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '162; setting to 0 instead 798s Warning: skipping read '162' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '162' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '163; setting to 0 instead 798s Warning: skipping read '163' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '163' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '164; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '165; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '166; setting to 0 instead 798s 166 reads; of these: 798s 166 (100.00%) were unpaired; of these: 798s 138 (83.13%) aligned 0 times 798s 12 (7.23%) aligned exactly 1 time 798s 16 (9.64%) aligned >1 times 798s 16.87% overall alignment rate 798s Read 50 alignments... 798s Read 100 alignments... 798s Read 150 alignments... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TACC 798s TACC 798s Processing line... 798s Processing line... 798s CCG 798s CCG 798s Processing line... 798s Processing line... 798s TC 798s TC 798s Processing line... 798s AAC 798s AAC 798s Processing line... 798s TC 798s TC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CAA 798s CAA 798s Processing line... 798s Processing line... 798s Processing line... 798s TC 798s TC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CC 798s CC 798s Processing line... 798s TACC 798s TACC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TTAA 798s TTAA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s AAC 798s AAC 798s Processing line... 798s AAT 798s AAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CGTGACAAC 798s CGTGACAAC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ATA 798s ATA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TC 798s TC 798s Processing line... 798s Processing line... 798s Processing line... 798s TC 798s TC 798s Processing line... 798s GACA 798s GACA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ATATC 798s ATATC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TCAACAA 798s TCAACAA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ACAA 798s ACAA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TACC 798s TACC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TACCACA 798s TACCACA 798s Processing line... 798s Processing line... 798s CGTCGTGACAACCCGA 798s CGTCGTGACAACCCGA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CG 798s CG 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CATTGGAA 798s CATTGGAA 798s Processing line... 798s CAATATC 798s CAATATC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CAATATCACAT 798s CAATATCACAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CGT 798s CGT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 28 alignments, 0 edits 798s --------------- 798s PASSED 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.2 798s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.1 798s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 3 798s *** Run 24 of 100 798s /usr/bin/bowtie2 --mm -a --rdg 39.9687341928214,3.04896583555364 --score-min L,8.71071751760831,4.54369633515095 --trim3 2 -N 0 -L20 --cp-ival 1 --np 2 -R 2 --large-index --cp-min 7 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 798s Reference gaps introduced: 1 798s Read gaps introduced: 0 798s Rearrangements introduced: 1 798s Created read sampler 798s Sampling 75 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 798s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '11' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 798s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '18' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 798s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '20' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 798s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '23' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 798s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '30' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 798s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '32' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 798s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '47' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 798s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '65' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 798s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '66' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 798s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '73' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 798s 75 reads; of these: 798s 75 (100.00%) were unpaired; of these: 798s 62 (82.67%) aligned 0 times 798s 8 (10.67%) aligned exactly 1 time 798s 5 (6.67%) aligned >1 times 798s 17.33% overall alignment rate 798s Read 50 alignments... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TTAA 798s TTAA 798s Processing line... 798s TTAA 798s TTAA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CTC 798s CTC 798s Processing line... 798s CTC 798s CTC 798s Processing line... 798s Processing line... 798s TCAT 798s TCAT 798s Processing line... 798s Processing line... 798s Processing line... 798s AACAACTCATT 798s AACAACTCATT 798s Processing line... 798s Processing line... 798s CGA 798s CGA 798s Processing line... 798s TCG 798s TCG 798s Processing line... 798s TCG 798s TCG 798s Processing line... 798s ACAATATC 798s ACAATATC 798s Processing line... 798s Processing line... 798s CC 798s CC 798s Processing line... 798s GG 798s GG 798s Processing line... 798s CC 798s CC 798s Processing line... 798s CC 798s CC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ATCAC 798s ATCAC 798s Processing line... 798s Processing line... 798s AACAACTCATTG 798s AACAACTCATTG 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CTG 798s CTG 798s Processing line... 798s Processing line... 798s Processing line... 798s TAAT 798s TAAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GTGAC 798s GTGAC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CAAC 798s CAAC 798s Processing line... 798s CAAC 798s CAAC 798s Processing line... 798s CAAC 798s CAAC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 22 alignments, 0 edits 798s --------------- 798s PASSED 798s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 798s /usr/bin/bowtie2 --mm -a --rdg 39.9687341928214,3.04896583555364 --score-min L,8.71071751760831,4.54369633515095 --trim3 2 -N 0 -L20 --cp-ival 1 --np 2 -R 2 --large-index --cp-min 7 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 798s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 798s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '11' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 798s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '18' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 798s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '20' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 798s Warning: skipping read '23' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '23' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 798s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '30' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 798s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '32' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 798s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 798s Warning: skipping read '47' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 798s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '65' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 798s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '66' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 798s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 798s Warning: skipping read '73' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 798s 75 reads; of these: 798s 75 (100.00%) were unpaired; of these: 798s 62 (82.67%) aligned 0 times 798s 8 (10.67%) aligned exactly 1 time 798s 5 (6.67%) aligned >1 times 798s 17.33% overall alignment rate 798s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.2 798s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.1 798s Introducing 1 SNPs, 0/0 ref/read gaps, and 2 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 8 798s Reference gaps introduced: 0 798s Read gaps introduced: 0 798s Rearrangements introduced: 2 798s Created read sampler 798s Sampling 73 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 798s *** Run 25 of 100 798s /usr/bin/bowtie2 -N 1 -L25 --mp 4.51432231893642,3.32156209057792 --cp-ival 1 --score-min L,5.03416405148057,8.24216257807977 --rdg 33.0351872383575 --rfg 7.28239807207316,13.8582782302767 --mm --cp-min 2 --large-index --norc --np 2 --trim5 7 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 798s Warning: skipping mate #2 of read '0' because length (1) <= # seed mismatches (1) 798s Warning: skipping mate #2 of read '0' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 798s Warning: skipping mate #2 of read '7' because length (1) <= # seed mismatches (1) 798s Warning: skipping mate #2 of read '7' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 798s Warning: skipping mate #1 of read '9' because length (1) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '9' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 798s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '12' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 798s Warning: skipping read '19' because length (1) <= # seed mismatches (1) 798s Warning: skipping read '19' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 798s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '21' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 798s Warning: skipping mate #1 of read '25' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '25' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 798s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '26' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 798s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '33' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 798s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '34' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 798s Warning: skipping mate #1 of read '36' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '36' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 798s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '38' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 798s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '44' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 798s Warning: skipping mate #2 of read '49' because length (1) <= # seed mismatches (1) 798s Warning: skipping mate #2 of read '49' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 798s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '54' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 798s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (1) 798s Warning: skipping mate #2 of read '60' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 798s Warning: skipping mate #1 of read '61' because length (1) <= # seed mismatches (1) 798s Warning: skipping mate #1 of read '61' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 798s 73 reads; of these: 798s 60 (82.19%) were paired; of these: 798s 60 (100.00%) aligned concordantly 0 times 798s 0 (0.00%) aligned concordantly exactly 1 time 798s 0 (0.00%) aligned concordantly >1 times 798s ---- 798s 60 pairs aligned concordantly 0 times; of these: 798s 0 (0.00%) aligned discordantly 1 time 798s ---- 798s 60 pairs aligned 0 times concordantly or discordantly; of these: 798s 120 mates make up the pairs; of these: 798s 112 (93.33%) aligned 0 times 798s 5 (4.17%) aligned exactly 1 time 798s 3 (2.50%) aligned >1 times 798s 13 (17.81%) were unpaired; of these: 798s 13 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 6.02% overall alignment rate 798s Read 50 alignments... 798s Read 100 alignments... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CGTG 798s CGTG 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TTA 798s TTA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CA 798s CA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GAC 798s GAC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ATAT 798s ATAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GTGAC 798s GTGAC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CAC 798s CAC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TC 798s TC 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 8 alignments, 0 edits 798s --------------- 798s PASSED 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.1 798s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.2 798s Introducing 2 SNPs, 0/1 ref/read gaps, and 2 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 5 798s Reference gaps introduced: 0 798s Read gaps introduced: 1 798s Rearrangements introduced: 2 798s Created read sampler 798s Sampling 42 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s *** Run 26 of 100 798s /usr/bin/bowtie2 --large-index --cp-min 2 --trim5 9 --trim3 3 --cp-ival 1 --local --n-ceil 0.0507184748123728,0.360520167576249 --mp 9.8476016554265,4.14909016931088 --mm -a --rfg 8.66533496116915,4.84300046910301 --rdg 40.4832067797299,6.05574382177472 --score-min L,7.83190323259299,9.67116293872188 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 798s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 798s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 798s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 798s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 798s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 798s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 798s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 798s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 798s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 798s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 798s 42 reads; of these: 798s 33 (78.57%) were paired; of these: 798s 33 (100.00%) aligned concordantly 0 times 798s 0 (0.00%) aligned concordantly exactly 1 time 798s 0 (0.00%) aligned concordantly >1 times 798s ---- 798s 33 pairs aligned concordantly 0 times; of these: 798s 0 (0.00%) aligned discordantly 1 time 798s ---- 798s 33 pairs aligned 0 times concordantly or discordantly; of these: 798s 66 mates make up the pairs; of these: 798s 66 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 9 (21.43%) were unpaired; of these: 798s 9 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 0.00% overall alignment rate 798s Read 50 alignments... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 0 alignments, 0 edits 798s --------------- 798s PASSED 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.2 798s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.1 798s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 7 798s Reference gaps introduced: 0 798s Read gaps introduced: 0 798s Rearrangements introduced: 1 798s Created read sampler 798s Sampling 29 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s *** Run 27 of 100 798s /usr/bin/bowtie2 --large-index --cp-min 8 --np 2 --norc -k 16 --local --cp-ival 1 -N 1 -L18 --mp 4.78575256969266,2.64326386697471 --trim3 0 --rfg 33.3524077716072,4.29567790037609 --rdg 28.5944271341554 --score-min L,3.51590885727306,5.00412819597446 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 798s Warning: skipping read '3' because length (1) <= # seed mismatches (1) 798s Warning: skipping read '3' because it was < 2 characters long 798s 29 reads; of these: 798s 29 (100.00%) were unpaired; of these: 798s 29 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 0.00% overall alignment rate 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 0 alignments, 0 edits 798s --------------- 798s PASSED 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.1 798s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.2 798s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 4 798s Reference gaps introduced: 0 798s Read gaps introduced: 0 798s Rearrangements introduced: 0 798s Created read sampler 798s Sampling 119 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s *** Run 28 of 100 798s /usr/bin/bowtie2 -i S,2.70504749609578 --ma 6.02714606901045 --cp-min 5 --large-index --score-min L,4.01757801533403,4.93345685971148 --rdg 19.0833047232967,18.2072293826446 --rfg 12.9233471911794 --cp-ival 1 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 798s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 798s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '28' because it was < 2 characters long 798s Warning: skipping mate #2 of read '28' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 798s Warning: skipping mate #1 of read '29' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '29' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 798s Read 50 alignments... 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 798s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #2 of read '94' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 798s Warning: skipping mate #1 of read '116' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '116' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 798s Read 100 alignments... 798s 119 reads; of these: 798s 119 (100.00%) were paired; of these: 798s 119 (100.00%) aligned concordantly 0 times 798s 0 (0.00%) aligned concordantly exactly 1 time 798s 0 (0.00%) aligned concordantly >1 times 798s ---- 798s 119 pairs aligned concordantly 0 times; of these: 798s 1 (0.84%) aligned discordantly 1 time 798s ---- 798s 118 pairs aligned 0 times concordantly or discordantly; of these: 798s 236 mates make up the pairs; of these: 798s 211 (89.41%) aligned 0 times 798s 17 (7.20%) aligned exactly 1 time 798s 8 (3.39%) aligned >1 times 798s 11.34% overall alignment rate 798s Read 150 alignments... 798s Read 200 alignments... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GGAAT 798s GGAAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CGTCGTGACAACCCGAA 798s CGTCGTGACAACCCGAA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CGTCGTGACAACCCGAA 798s CGTCGTGACAACCCGAA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GACAA 798s GACAA 798s Processing line... 798s Processing line... 798s AATATCACA 798s AATATCACA 798s Processing line... 798s Processing line... 798s CAATATCA 798s CAATATCA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ACAT 798s ACAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GTGA 798s GTGA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CC 798s CC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CC 798s CC 798s Processing line... 798s Processing line... 798s AATAT 798s AATAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CACAATATCACA 798s CACAATATCACA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TA 798s TA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TCGTGACAAC 798s TCGTGACAAC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s AC 798s AC 798s Processing line... 798s Processing line... 798s CCCGAA 798s CCCGAA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GTGACAACCCGAAC 798s GTGACAACCCGAAC 798s Processing line... 798s ATCACAT 798s ATCACAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s AATATCACA 798s AATATCACA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CAATATCACAT 798s CAATATCACAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ACAACCC 798s ACAACCC 798s Processing line... 798s Processing line... 798s AATATC 798s AATATC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CG 798s CG 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GTCGTGACAACCC 798s GTCGTGACAACCC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GTGACAACCC 798s GTGACAACCC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s GG 798s GG 798s Processing line... 798s Processing line... 798s CGA 798s CGA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 27 alignments, 0 edits 798s --------------- 798s PASSED 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.1 798s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.2 798s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 6 798s Reference gaps introduced: 1 798s Read gaps introduced: 0 798s Rearrangements introduced: 0 798s Created read sampler 798s Sampling 96 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting*** Run 29 of 100 798s /usr/bin/bowtie2 --cp-min 2 --large-index --ma 39.205606597232 --cp-ival 1 --n-ceil 1.26361451433377,1.04035695173328 --nofw --mp 3.67233446759564,1.60297198046586 -a --score-min L,3.74464181312106,5.68754534862999 --rdg 21.9367654340458,2.92819677940417 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 798s 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 798s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '5' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 798s Warning: skipping mate #1 of read '23' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '23' because it was < 2 characters long 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 798s Read 50 alignments... 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 798s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 798s Read 100 alignments... 798s 96 reads; of these: 798s 96 (100.00%) were paired; of these: 798s 96 (100.00%) aligned concordantly 0 times 798s 0 (0.00%) aligned concordantly exactly 1 time 798s 0 (0.00%) aligned concordantly >1 times 798s ---- 798s 96 pairs aligned concordantly 0 times; of these: 798s 1 (1.04%) aligned discordantly 1 time 798s ---- 798s 95 pairs aligned 0 times concordantly or discordantly; of these: 798s 190 mates make up the pairs; of these: 798s 176 (92.63%) aligned 0 times 798s 9 (4.74%) aligned exactly 1 time 798s 5 (2.63%) aligned >1 times 798s 8.33% overall alignment rate 798s Read 150 alignments... 798s Read 200 alignments... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TTC 798s TTC 798s Processing line... 798s ACCA 798s ACCA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TACCA 798s TACCA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s AACCC 798s AACCC 798s Processing line... 798s Processing line... 798s AA 798s AA 798s Processing line... 798s AA 798s AA 798s Processing line... 798s AA 798s AA 798s Processing line... 798s AA 798s AA 798s Processing line... 798s AA 798s AA 798s Processing line... 798s AA 798s AA 798s Processing line... 798s AA 798s AA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TCA 798s TCA 798s Processing line... 798s TCA 798s TCA 798s Processing line... 798s TCA 798s TCA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s AC 798s AC 798s Processing line... 798s AC 798s AC 798s Processing line... 798s AC 798s AC 798s Processing line... 798s AC 798s AC 798s Processing line... 798s AC 798s AC 798s Processing line... 798s AC 798s AC 798s Processing line... 798s AC 798s AC 798s Processing line... 798s AC 798s AC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CAACAACTCATTGGAAT 798s CAACAACTCATTGGAAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ATTG 798s ATTG 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s TACCACAA 798s TACCACAA 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s ACAAT 798s ACAAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CT 798s CT 798s Processing line... 798s CT 798s CT 798s Processing line... 798s CT 798s CT 798s Processing line... 798s CT 798s CT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s AATAT 798s AATAT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s CCC 798s CCC 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s AT 798s AT 798s Processing line... 798s AT 798s AT 798s Processing line... 798s AT 798s AT 798s Processing line... 798s AT 798s AT 798s Processing line... 798s AT 798s AT 798s Processing line... 798s AT 798s AT 798s Processing line... 798s AT 798s AT 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s AACT 798s AACT 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 40 alignments, 0 edits 798s --------------- 798s PASSED 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.1 798s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.2 798s Introducing 8 SNPs, 0/1 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 8 798s Reference gaps introduced: 0 798s Read gaps introduced: 2 798s Rearrangements introduced: 0 798s Created read sampler 798s Sampling 42 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s *** Run 30 of 100 798s /usr/bin/bowtie2 --rfg 35.5126714825524,10.1617842417917 --score-min L,5.62368759466961,2.97360536677598 --trim3 1 --mp 9.13708223386295,3.07791524316314 --n-ceil 1.03895795685771,0.374000586704374 --cp-ival 2 --local -k 5 --np 4 --large-index --cp-min 2 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 798s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '13' because it was < 2 characters long 798s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '14' because it was < 2 characters long 798s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '20' because it was < 2 characters long 798s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '27' because it was < 2 characters long 798s 42 reads; of these: 798s 42 (100.00%) were paired; of these: 798s 42 (100.00%) aligned concordantly 0 times 798s 0 (0.00%) aligned concordantly exactly 1 time 798s 0 (0.00%) aligned concordantly >1 times 798s ---- 798s 42 pairs aligned concordantly 0 times; of these: 798s 0 (0.00%) aligned discordantly 1 time 798s ---- 798s 42 pairs aligned 0 times concordantly or discordantly; of these: 798s 84 mates make up the pairs; of these: 798s 84 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 0.00% overall alignment rate 798s Read 50 alignments... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s Processing line... 798s --- Summary --- 798s Read 1 reference strings 798s Checked 0 alignments, 0 edits 798s --------------- 798s PASSED 798s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 798s /usr/bin/bowtie2 --rfg 35.5126714825524,10.1617842417917 --score-min L,5.62368759466961,2.97360536677598 --trim3 1 --mp 9.13708223386295,3.07791524316314 --n-ceil 1.03895795685771,0.374000586704374 --cp-ival 2 --local -k 5 --np 4 --large-index --cp-min 2 -r -p 3 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 798s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '13' because it was < 2 characters long 798s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '14' because it was < 2 characters long 798s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '20' because it was < 2 characters long 798s Warning: skipping mate #1 of read '27' because length (1) <= # seed mismatches (0) 798s Warning: skipping mate #1 of read '27' because it was < 2 characters long 798s 42 reads; of these: 798s 42 (100.00%) were paired; of these: 798s 42 (100.00%) aligned concordantly 0 times 798s 0 (0.00%) aligned concordantly exactly 1 time 798s 0 (0.00%) aligned concordantly >1 times 798s ---- 798s 42 pairs aligned concordantly 0 times; of these: 798s 0 (0.00%) aligned discordantly 1 time 798s ---- 798s 42 pairs aligned 0 times concordantly or discordantly; of these: 798s 84 mates make up the pairs; of these: 798s 84 (100.00%) aligned 0 times 798s 0 (0.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 0.00% overall alignment rate 798s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 798s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 798s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 798s Flattened IUPAC characters 798s Mutating sequence Sim.pm.1 798s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutating sequence Sim.pm.2 798s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 798s Finished SNPs 798s Finished ref gaps 798s Finished read gaps 798s Mutated reference genome to subject genome 798s SNPs introduced: 1 798s Reference gaps introduced: 1 798s Read gaps introduced: 1 798s Rearrangements introduced: 0 798s Created read sampler 798s Sampling 83 reads 798s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 798s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 798s parsing sequence Sim.pm.1... 798s parsing sequence Sim.pm.2... 798s Parsed 78 reference bases 798s *** Run 31 of 100 798s /usr/bin/bowtie2 --large-index --cp-min 6 -k 5 --np 1 --norc --trim3 1 --cp-ival 2 --mm --rfg 49.5450309130026,12.8409876350704 --score-min L,9.36307470540579,3.80343796605814 --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 799s 83 reads; of these: 799s 83 (100.00%) were unpaired; of these: 799s 79 (95.18%) aligned 0 times 799s 4 (4.82%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 4.82% overall alignment rate 799s Read 50 alignments... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s CTG 799s CTG 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s ACCACAATAT 799s ACCACAATAT 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s GAC 799s GAC 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s TACC 799s TACC 799s Processing line... 799s Processing line... 799s Processing line... 799s --- Summary --- 799s Read 1 reference strings 799s Checked 4 alignments, 0 edits 799s --------------- 799s PASSED 799s ALSO checking that bowtie2 and bowtie2-align match up 799s /usr/bin/bowtie2 --large-index --cp-min 6 -k 5 --np 1 --norc --trim3 1 --cp-ival 2 --mm --rfg 49.5450309130026,12.8409876350704 --score-min L,9.36307470540579,3.80343796605814 --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 799s 83 reads; of these: 799s 83 (100.00%) were unpaired; of these: 799s 79 (95.18%) aligned 0 times 799s 4 (4.82%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 4.82% overall alignment rate 799s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 799s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 799s /usr/bin/bowtie2 --large-index --cp-min 6 -k 5 --np 1 --norc --trim3 1 --cp-ival 2 --mm --rfg 49.5450309130026,12.8409876350704 --score-min L,9.36307470540579,3.80343796605814 --qseq -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 799s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 799s 83 reads; of these: 799s 83 (100.00%) were unpaired; of these: 799s 79 (95.18%) aligned 0 times 799s 4 (4.82%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 4.82% overall alignment rate 799s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 799s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 799s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 799s Flattened IUPAC characters 799s Mutating sequence Sim.pm.2 799s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutating sequence Sim.pm.1 799s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutated reference genome to subject genome 799s SNPs introduced: 11 799s Reference gaps introduced: 0 799s Read gaps introduced: 2 799s Rearrangements introduced: 0 799s Created read sampler 799s Sampling 137 reads 799s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 799s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 799s parsing sequence Sim.pm.1... 799s parsing sequence Sim.pm.2... 799s *** Run 32 of 100 799s /usr/bin/bowtie2 -k 7 -i C,2.10959734363285 --trim5 7 --norc -R 1 --cp-min 4 --large-index --ma 32.1196234194413 --score-min L,9.32195382861704,2.98386202129921 --trim3 0 --cp-ival 2 --nofw -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 799s Parsed 78 reference bases 799s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 799s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 799s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '10' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 799s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '17' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 799s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '28' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 799s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '29' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 799s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '32' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 799s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '34' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 799s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '35' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 799s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '42' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 799s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '47' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 799s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '49' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 799s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '53' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 799s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '54' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 799s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '55' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 799s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '59' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 799s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '62' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 799s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '64' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 799s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '67' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 799s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '68' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 799s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '72' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 799s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '74' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 799s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '77' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 799s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '81' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 799s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '82' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 799s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '86' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 799s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '87' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 799s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '88' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 799s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '90' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 799s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '95' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 799s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '98' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 799s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '101' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 799s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '102' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 799s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '105' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 799s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '111' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 799s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '114' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 799s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '116' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 799s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '121' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 799s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '122' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 799s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '123' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 799s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '124' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 799s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '133' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 799s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '135' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 799s 137 reads; of these: 799s 137 (100.00%) were unpaired; of these: 799s 137 (100.00%) aligned 0 times 799s 0 (0.00%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 0.00% overall alignment rate 799s Read 50 alignments... 799s Read 100 alignments... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s --- Summary --- 799s Read 1 reference strings 799s Checked 0 alignments, 0 edits 799s --------------- 799s PASSED 799s ALSO checking that bowtie2 and bowtie2-align match up 799s /usr/bin/bowtie2 -k 7 -i C,2.10959734363285 --trim5 7 --norc -R 1 --cp-min 4 --large-index --ma 32.1196234194413 --score-min L,9.32195382861704,2.98386202129921 --trim3 0 --cp-ival 2 --nofw -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 799s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 799s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 799s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '10' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 799s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '17' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 799s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '28' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 799s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '29' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 799s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '32' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 799s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '34' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 799s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '35' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 799s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '42' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 799s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '47' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 799s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '49' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 799s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '53' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 799s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '54' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 799s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '55' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 799s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '59' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 799s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '62' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 799s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '64' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 799s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '67' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 799s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '68' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 799s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '72' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 799s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '74' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 799s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '77' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 799s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '81' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 799s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '82' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 799s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '86' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 799s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '87' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 799s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '88' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 799s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '90' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 799s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '95' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 799s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '98' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 799s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '101' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 799s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '102' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 799s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '105' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 799s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '111' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 799s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '114' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 799s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '116' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 799s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '121' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 799s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '122' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 799s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '123' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 799s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '124' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 799s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '133' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 799s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '135' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 799s 137 reads; of these: 799s 137 (100.00%) were unpaired; of these: 799s 137 (100.00%) aligned 0 times 799s 0 (0.00%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 0.00% overall alignment rate 799s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 799s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 799s /usr/bin/bowtie2 -k 7 -i C,2.10959734363285 --trim5 7 --norc -R 1 --cp-min 4 --large-index --ma 32.1196234194413 --score-min L,9.32195382861704,2.98386202129921 --trim3 0 --cp-ival 2 --nofw -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 799s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 799s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 799s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '10' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 799s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '17' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 799s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '28' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 799s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '29' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 799s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '32' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 799s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '34' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 799s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '35' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 799s Warning: skipping read '42' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '42' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 799s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '47' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 799s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '49' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 799s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '53' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 799s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '54' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 799s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '55' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 799s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '59' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 799s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '62' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 799s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '64' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 799s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '67' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 799s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '68' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 799s Warning: skipping read '72' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '72' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 799s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '74' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 799s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '77' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 799s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '81' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 799s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '82' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 799s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '86' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 799s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '87' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 799s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '88' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 799s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '90' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 799s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '95' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 799s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '98' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 799s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '101' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 799s Warning: skipping read '102' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '102' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 799s Warning: skipping read '105' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '105' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 799s Warning: skipping read '111' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '111' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 799s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '114' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 799s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '116' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 799s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '121' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 799s Warning: skipping read '122' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '122' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 799s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '123' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 799s Warning: skipping read '124' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '124' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 799s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '133' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 799s Warning: skipping read '135' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '135' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 799s 137 reads; of these: 799s 137 (100.00%) were unpaired; of these: 799s 137 (100.00%) aligned 0 times 799s 0 (0.00%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 0.00% overall alignment rate 799s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 799s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 799s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 799s Flattened IUPAC characters 799s Mutating sequence Sim.pm.2 799s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutating sequence Sim.pm.1 799s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutated reference genome to subject genome 799s SNPs introduced: 0 799s Reference gaps introduced: 0 799s Read gaps introduced: 1 799s Rearrangements introduced: 0 799s Created read sampler 799s Sampling 64 reads 799s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 799s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 799s parsing sequence Sim.pm.1... 799s parsing sequence Sim.pm.2... 799s Parsed 78 reference bases 799s *** Run 33 of 100 799s /usr/bin/bowtie2 -M 7 --score-min L,7.88556118229064,3.78309899222265 --norc --np 3 --cp-min 3 --cp-ival 1 --local --large-index -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 799s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 799s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '1' because it was < 2 characters long 799s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '16' because it was < 2 characters long 799s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #1 of read '20' because it was < 2 characters long 799s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '26' because it was < 2 characters long 799s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '31' because it was < 2 characters long 799s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '56' because it was < 2 characters long 799s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #1 of read '63' because it was < 2 characters long 799s 64 reads; of these: 799s 64 (100.00%) were paired; of these: 799s 64 (100.00%) aligned concordantly 0 times 799s 0 (0.00%) aligned concordantly exactly 1 time 799s 0 (0.00%) aligned concordantly >1 times 799s ---- 799s 64 pairs aligned concordantly 0 times; of these: 799s 0 (0.00%) aligned discordantly 1 time 799s ---- 799s 64 pairs aligned 0 times concordantly or discordantly; of these: 799s 128 mates make up the pairs; of these: 799s 128 (100.00%) aligned 0 times 799s 0 (0.00%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 0.00% overall alignment rate 799s Read 50 alignments... 799s Read 100 alignments... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s --- Summary --- 799s Read 1 reference strings 799s Checked 0 alignments, 0 edits 799s --------------- 799s PASSED 799s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 799s /usr/bin/bowtie2 -M 7 --score-min L,7.88556118229064,3.78309899222265 --norc --np 3 --cp-min 3 --cp-ival 1 --local --large-index -q -p 3 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 799s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 799s Warning: skipping mate #2 of read '1' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '1' because it was < 2 characters long 799s Warning: skipping mate #2 of read '16' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '16' because it was < 2 characters long 799s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #1 of read '20' because it was < 2 characters long 799s Warning: skipping mate #2 of read '26' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '26' because it was < 2 characters long 799s Warning: skipping mate #2 of read '31' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '31' because it was < 2 characters long 799s Warning: skipping mate #2 of read '56' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #2 of read '56' because it was < 2 characters long 799s Warning: skipping mate #1 of read '63' because length (1) <= # seed mismatches (0) 799s Warning: skipping mate #1 of read '63' because it was < 2 characters long 799s 64 reads; of these: 799s 64 (100.00%) were paired; of these: 799s 64 (100.00%) aligned concordantly 0 times 799s 0 (0.00%) aligned concordantly exactly 1 time 799s 0 (0.00%) aligned concordantly >1 times 799s ---- 799s 64 pairs aligned concordantly 0 times; of these: 799s 0 (0.00%) aligned discordantly 1 time 799s ---- 799s 64 pairs aligned 0 times concordantly or discordantly; of these: 799s 128 mates make up the pairs; of these: 799s 128 (100.00%) aligned 0 times 799s 0 (0.00%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 0.00% overall alignment rate 799s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 799s *** Run 34 of 100 799s /usr/bin/bowtie2 --large-index --cp-min 2 -R 1 --np 1 --trim5 9 -M 3 --cp-ival 1 --n-ceil 0.00568616598999319,0.124257731745908 --local -N 0 -L26 --nofw --trim3 6 --score-min L,5.17810080579415,7.7784243077813 --mm -r -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw 799s Flattened IUPAC characters 799s Mutating sequence Sim.pm.1 799s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutating sequence Sim.pm.2 799s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutated reference genome to subject genome 799s SNPs introduced: 1 799s Reference gaps introduced: 1 799s Read gaps introduced: 1 799s Rearrangements introduced: 0 799s Created read sampler 799s Sampling 110 reads 799s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 799s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 799s parsing sequence Sim.pm.1... 799s parsing sequence Sim.pm.2... 799s Parsed 78 reference bases 799s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 799s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '0' because it was < 2 characters long 799s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '1' because it was < 2 characters long 799s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '2' because it was < 2 characters long 799s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '12' because it was < 2 characters long 799s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '15' because it was < 2 characters long 799s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '16' because it was < 2 characters long 799s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '19' because it was < 2 characters long 799s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '20' because it was < 2 characters long 799s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '22' because it was < 2 characters long 799s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '24' because it was < 2 characters long 799s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '26' because it was < 2 characters long 799s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '27' because it was < 2 characters long 799s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '28' because it was < 2 characters long 799s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '37' because it was < 2 characters long 799s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '39' because it was < 2 characters long 799s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '40' because it was < 2 characters long 799s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '46' because it was < 2 characters long 799s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '52' because it was < 2 characters long 799s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '53' because it was < 2 characters long 799s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '54' because it was < 2 characters long 799s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '57' because it was < 2 characters long 799s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '59' because it was < 2 characters long 799s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '60' because it was < 2 characters long 799s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '61' because it was < 2 characters long 799s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '62' because it was < 2 characters long 799s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '63' because it was < 2 characters long 799s Warning: skipping read '67' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '67' because it was < 2 characters long 799s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '68' because it was < 2 characters long 799s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '70' because it was < 2 characters long 799s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '72' because it was < 2 characters long 799s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '73' because it was < 2 characters long 799s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '74' because it was < 2 characters long 799s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '77' because it was < 2 characters long 799s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '78' because it was < 2 characters long 799s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '80' because it was < 2 characters long 799s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '81' because it was < 2 characters long 799s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '86' because it was < 2 characters long 799s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '91' because it was < 2 characters long 799s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '93' because it was < 2 characters long 799s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '94' because it was < 2 characters long 799s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '95' because it was < 2 characters long 799s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '98' because it was < 2 characters long 799s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '99' because it was < 2 characters long 799s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '100' because it was < 2 characters long 799s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '103' because it was < 2 characters long 799s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '104' because it was < 2 characters long 799s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '106' because it was < 2 characters long 799s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '108' because it was < 2 characters long 799s 110 reads; of these: 799s 110 (100.00%) were unpaired; of these: 799s 110 (100.00%) aligned 0 times 799s 0 (0.00%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 0.00% overall alignment rate 799s Read 50 alignments... 799s Read 100 alignments... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s /usr/bin/bowtie2 --large-index --cp-min 2 -R 1 --np 1 --trim5 9 -M 3 --cp-ival 1 --n-ceil 0.00568616598999319,0.124257731745908 --local -N 0 -L26 --nofw --trim3 6 --score-min L,5.17810080579415,7.7784243077813 --mm -r -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s --- Summary --- 799s Read 1 reference strings 799s Checked 0 alignments, 0 edits 799s --------------- 799s PASSED 799s ALSO checking that bowtie2 and bowtie2-align match up 799s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 799s Warning: skipping read '0' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '0' because it was < 2 characters long 799s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '1' because it was < 2 characters long 799s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '2' because it was < 2 characters long 799s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '12' because it was < 2 characters long 799s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '15' because it was < 2 characters long 799s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '16' because it was < 2 characters long 799s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '19' because it was < 2 characters long 799s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '20' because it was < 2 characters long 799s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '22' because it was < 2 characters long 799s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '24' because it was < 2 characters long 799s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '26' because it was < 2 characters long 799s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '27' because it was < 2 characters long 799s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '28' because it was < 2 characters long 799s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '37' because it was < 2 characters long 799s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '39' because it was < 2 characters long 799s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '40' because it was < 2 characters long 799s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '46' because it was < 2 characters long 799s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '52' because it was < 2 characters long 799s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '53' because it was < 2 characters long 799s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '54' because it was < 2 characters long 799s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '57' because it was < 2 characters long 799s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '59' because it was < 2 characters long 799s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '60' because it was < 2 characters long 799s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '61' because it was < 2 characters long 799s Warning: skipping read '62' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '62' because it was < 2 characters long 799s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '63' because it was < 2 characters long 799s Warning: skipping read '67' because length (1) <= # seed mismatches (0) 799s Warning: skipping read '67' because it was < 2 characters long 799s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '68' because it was < 2 characters long 799s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '70' because it was < 2 characters long 799s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '72' because it was < 2 characters long 799s Warning: skipping read '73' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '73' because it was < 2 characters long 799s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '74' because it was < 2 characters long 799s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '77' because it was < 2 characters long 799s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '78' because it was < 2 characters long 799s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 799s *** Run 35 of 100 799s /usr/bin/bowtie2 --score-min L,2.59474570050528,6.70199799755115 --gbar 3 -N 1 -L16 --mp 9.40163307503742,9.26670907143051 --n-ceil 0.361175665957821,0.999450391136708 --cp-ival 2 --np 1 --trim5 3 --ma 7.04207556302493 --cp-min 6 --large-index -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 799s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '80' because it was < 2 characters long 799s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '81' because it was < 2 characters long 799s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '86' because it was < 2 characters long 799s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '91' because it was < 2 characters long 799s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '93' because it was < 2 characters long 799s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '94' because it was < 2 characters long 799s Warning: skipping read '95' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '95' because it was < 2 characters long 799s Warning: skipping read '98' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '98' because it was < 2 characters long 799s Warning: skipping read '99' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '99' because it was < 2 characters long 799s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '100' because it was < 2 characters long 799s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '103' because it was < 2 characters long 799s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '104' because it was < 2 characters long 799s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '106' because it was < 2 characters long 799s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '108' because it was < 2 characters long 799s 110 reads; of these: 799s 110 (100.00%) were unpaired; of these: 799s 110 (100.00%) aligned 0 times 799s 0 (0.00%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 0.00% overall alignment rate 799s Flattened IUPAC characters 799s Mutating sequence Sim.pm.1 799s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutating sequence Sim.pm.2 799s Introducing 2 SNPs, 0/0 ref/read gaps, and 3 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutated reference genome to subject genome 799s SNPs introduced: 5 799s Reference gaps introduced: 1 799s Read gaps introduced: 0 799s Rearrangements introduced: 4 799s Created read sampler 799s Sampling 8 reads 799s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 799s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 799s parsing sequence Sim.pm.1... 799s parsing sequence Sim.pm.2... 799s Parsed 78 reference bases 799s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting/usr/bin/bowtie2 --score-min L,2.59474570050528,6.70199799755115 --gbar 3 -N 1 -L16 --mp 9.40163307503742,9.26670907143051 --n-ceil 0.361175665957821,0.999450391136708 --cp-ival 2 --np 1 --trim5 3 --ma 7.04207556302493 --cp-min 6 --large-index -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 799s 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 799s 8 reads; of these: 799s 8 (100.00%) were paired; of these: 799s 8 (100.00%) aligned concordantly 0 times 799s 0 (0.00%) aligned concordantly exactly 1 time 799s 0 (0.00%) aligned concordantly >1 times 799s ---- 799s 8 pairs aligned concordantly 0 times; of these: 799s 0 (0.00%) aligned discordantly 1 time 799s ---- 799s 8 pairs aligned 0 times concordantly or discordantly; of these: 799s 16 mates make up the pairs; of these: 799s 14 (87.50%) aligned 0 times 799s 1 (6.25%) aligned exactly 1 time 799s 1 (6.25%) aligned >1 times 799s 12.50% overall alignment rate 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s CA 799s CA 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s TTCGTCGTGACAACCC 799s TTCGTCGTGACAACCC 799s Processing line... 799s --- Summary --- 799s Read 1 reference strings 799s Checked 2 alignments, 0 edits 799s --------------- 799s PASSED 799s ALSO checking that bowtie2 and bowtie2-align match up 799s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 799s 8 reads; of these: 799s 8 (100.00%) were paired; of these: 799s 8 (100.00%) aligned concordantly 0 times 799s 0 (0.00%) aligned concordantly exactly 1 time 799s 0 (0.00%) aligned concordantly >1 times 799s ---- 799s 8 pairs aligned concordantly 0 times; of these: 799s 0 (0.00%) aligned discordantly 1 time 799s ---- 799s 8 pairs aligned 0 times concordantly or discordantly; of these: 799s 16 mates make up the pairs; of these: 799s 14 (87.50%) aligned 0 times 799s 1 (6.25%) aligned exactly 1 time 799s 1 (6.25%) aligned >1 times 799s 12.50% overall alignment rate 799s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 799s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 799s /usr/bin/bowtie2 --score-min L,2.59474570050528,6.70199799755115 --gbar 3 -N 1 -L16 --mp 9.40163307503742,9.26670907143051 --n-ceil 0.361175665957821,0.999450391136708 --cp-ival 2 --np 1 --trim5 3 --ma 7.04207556302493 --cp-min 6 --large-index -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 799s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 799s 8 reads; of these: 799s 8 (100.00%) were paired; of these: 799s 8 (100.00%) aligned concordantly 0 times 799s 0 (0.00%) aligned concordantly exactly 1 time 799s 0 (0.00%) aligned concordantly >1 times 799s ---- 799s 8 pairs aligned concordantly 0 times; of these: 799s 0 (0.00%) aligned discordantly 1 time 799s ---- 799s 8 pairs aligned 0 times concordantly or discordantly; of these: 799s 16 mates make up the pairs; of these: 799s 14 (87.50%) aligned 0 times 799s 1 (6.25%) aligned exactly 1 time 799s 1 (6.25%) aligned >1 times 799s 12.50% overall alignment rate 799s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 799s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 799s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 799s Flattened IUPAC characters 799s Mutating sequence Sim.pm.2 799s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutating sequence Sim.pm.1 799s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutated reference genome to subject genome 799s SNPs introduced: 6 799s Reference gaps introduced: 0 799s Read gaps introduced: 1 799s Rearrangements introduced: 0 799s Created read sampler 799s Sampling 15 reads 799s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 799s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 799s parsing sequence Sim.pm.1... 799s parsing sequence Sim.pm.2... 799s Parsed 78 reference bases 799s *** Run 36 of 100 799s /usr/bin/bowtie2 --large-index --cp-min 3 -R 1 --norc --trim5 6 -k 2 --mp 7.43346384626088,3.57498435390818 -N 1 -L13 --cp-ival 1 --local --trim3 4 --rdg 9.58391349279911 --score-min L,4.46827807966789,2.60723026917063 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 799s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 799s Warning: skipping read '4' because it was < 2 characters long 799s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 799s Warning: skipping read '8' because it was < 2 characters long 799s Warning: skipping read '11' because length (1) <= # seed mismatches (1) 799s Warning: skipping read '11' because it was < 2 characters long 799s Warning: skipping read '12' because length (1) <= # seed mismatches (1) 799s Warning: skipping read '12' because it was < 2 characters long 799s Warning: skipping read '13' because length (1) <= # seed mismatches (1) 799s Warning: skipping read '13' because it was < 2 characters long 799s 15 reads; of these: 799s 15 (100.00%) were unpaired; of these: 799s 15 (100.00%) aligned 0 times 799s 0 (0.00%) aligned exactly 1 time 799s 0 (0.00%) aligned >1 times 799s 0.00% overall alignment rate 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s --- Summary --- 799s Read 1 reference strings 799s Checked 0 alignments, 0 edits 799s --------------- 799s PASSED 799s Flattened IUPAC characters 799s Mutating sequence Sim.pm.2 799s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutating sequence Sim.pm.1 799s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 799s Finished SNPs 799s Finished ref gaps 799s Finished read gaps 799s Mutated reference genome to subject genome 799s SNPs introduced: 6 799s Reference gaps introduced: 0 799s Read gaps introduced: 0 799s Rearrangements introduced: 0 799s Created read sampler 799s Sampling 33 reads 799s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 799s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 799s parsing sequence Sim.pm.1... 799s parsing sequence Sim.pm.2... 799s Parsed 78 reference bases 799s *** Run 37 of 100 799s /usr/bin/bowtie2 --mm --rdg 6.0579742588698 --score-min L,5.54657709992447,4.16094244489451 --cp-ival 1 -N 0 -L23 --trim5 5 -M 3 --np 2 --large-index --cp-min 3 --ma 20.6284346116786 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 799s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 799s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 799s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 799s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '4' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 799s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '8' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 799s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '11' because it was < 2 characters long 799s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 799s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 799s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 799s Warning: skipping read '33' because it was < 2 characters long 799s 33 reads; of these: 799s 33 (100.00%) were unpaired; of these: 799s 27 (81.82%) aligned 0 times 799s 4 (12.12%) aligned exactly 1 time 799s 2 (6.06%) aligned >1 times 799s 18.18% overall alignment rate 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s CAAC 799s CAAC 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s CA 799s CA 799s Processing line... 799s Processing line... 799s Processing line... 799s Processing line... 799s ATATC 799s ATATC 799s Processing line... 799s Processing line... 800s /usr/bin/bowtie2 --mm --rdg 6.0579742588698 --score-min L,5.54657709992447,4.16094244489451 --cp-ival 1 -N 0 -L23 --trim5 5 -M 3 --np 2 --large-index --cp-min 3 --ma 20.6284346116786 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CACAAT 800s CACAAT 800s Processing line... 800s Processing line... 800s TACCACAATATCACATT 800s TACCACAATATCACATT 800s Processing line... 800s Processing line... 800s ATATCAC 800s ATATCAC 800s Processing line... 800s --- Summary --- 800s Read 1 reference strings 800s Checked 6 alignments, 0 edits 800s --------------- 800s PASSED 800s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 800s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 800s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 800s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 800s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '4' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 800s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '8' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 800s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '11' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 800s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '33' because it was < 2 characters long 800s 33 reads; of these: 800s 33 (100.00%) were unpaired; of these: 800s 27 (81.82%) aligned 0 times 800s 4 (12.12%) aligned exactly 1 time 800s 2 (6.06%) aligned >1 times 800s 18.18% overall alignment rate 800s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 800s Flattened IUPAC characters 800s Mutating sequence Sim.pm.1 800s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutating sequence Sim.pm.2 800s Introducing 2 SNPs, 1/3 ref/read gaps, and 3 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutated reference genome to subject genome 800s SNPs introduced: 3 800s Reference gaps introduced: 1 800s Read gaps introduced: 4 800s Rearrangements introduced: 4 800s Created read sampler 800s Sampling 115 reads 800s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 800s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 800s parsing sequence Sim.pm.1... 800s parsing sequence Sim.pm.2... 800s Parsed 78 reference bases 800s *** Run 38 of 100 800s /usr/bin/bowtie2 --mm --score-min L,6.27882730201833,3.06213419338754 --rdg 43.6772405186507 --ma 36.5160794709189 --cp-min 2 --cp-ival 4 --large-index --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 800s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 800s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 800s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 800s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 800s Read 50 alignments... 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 800s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 800s Read 100 alignments... 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 800s Warning: skipping mate #2 of read 'R_1_1_1_111_111_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 800s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 800s Read 150 alignments... 800s 115 Read 200 alignments... 800s reads; of these: 800s 115 (100.00%) were paired; of these: 800s 114 (99.13%) aligned concordantly 0 times 800s 0 (0.00%) aligned concordantly exactly 1 time 800s 1 (0.87%) aligned concordantly >1 times 800s ---- 800s 114 pairs aligned concordantly 0 times; of these: 800s 1 (0.88%) aligned discordantly 1 time 800s ---- 800s 113 pairs aligned 0 times concordantly or discordantly; of these: 800s 226 mates make up the pairs; of these: 800s 202 (89.38%) aligned 0 times 800s 14 (6.19%) aligned exactly 1 time 800s 10 (4.42%) aligned >1 times 800s 12.17% overall alignment rate 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s TACCACAATATCACATT 800s TACCACAATATCACATT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s AC 800s AC 800s Processing line... 800s Processing line... 800s CA 800s CA 800s Processing line... 800s Processing line... 800s TTAA 800s TTAA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s TATCACAT 800s TATCACAT 800s Processing line... 800s Processing line... 800s TAT 800s TAT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CAACAA 800s CAACAA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s ACAA 800s ACAA 800s Processing line... 800s Processing line... 800s CACAT 800s CACAT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s AATATCA 800s AATATCA 800s Processing line... 800s Processing line... 800s AATATCACAT 800s AATATCACAT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s ACAA 800s ACAA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CAAT 800s CAAT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CAACCCGA 800s CAACCCGA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s TATC 800s TATC 800s Processing line... 800s Processing line... 800s CC 800s CC 800s Processing line... 800s CC 800s CC 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CCACAATATCACA 800s CCACAATATCACA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s TC 800s TC 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CCACA 800s CCACA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s GTGACAAC 800s GTGACAAC 800s Processing line... 800s ATCACA 800s ATCACA 800s Processing line... 800s Processing line... 800s Processing line... 800s TC 800s TC 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CA 800s CA 800s Processing line... 800s Processing line... 800s /usr/bin/bowtie2 --mm --score-min L,6.27882730201833,3.06213419338754 --rdg 43.6772405186507 --ma 36.5160794709189 --cp-min 2 --cp-ival 4 --large-index --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 800s Processing line... 800s Processing line... 800s ACAACCC 800s ACAACCC 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s GGA 800s GGA 800s Processing line... 800s Processing line... 800s CACAT 800s CACAT 800s Processing line... 800s Processing line... 800s TCATTGGAA 800s TCATTGGAA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s --- Summary --- 800s Read 1 reference strings 800s Checked 28 alignments, 0 edits 800s --------------- 800s PASSED 800s ALSO checking that bowtie2 and bowtie2-align match up 800s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 800s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 800s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 800s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 800s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 800s Warning: skipping mate #2 of read 'R_1_1_1_111_111_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 800s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read 'R_1_1_1_114_114_1/1' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 800s 115 reads; of these: 800s 115 (100.00%) were paired; of these: 800s 114 (99.13%) aligned concordantly 0 times 800s 0 (0.00%) aligned concordantly exactly 1 time 800s 1 (0.87%) aligned concordantly >1 times 800s ---- 800s 114 pairs aligned concordantly 0 times; of these: 800s 1 (0.88%) aligned discordantly 1 time 800s ---- 800s 113 pairs aligned 0 times concordantly or discordantly; of these: 800s 226 mates make up the pairs; of these: 800s 202 (89.38%) aligned 0 times 800s 14 (6.19%) aligned exactly 1 time 800s 10 (4.42%) aligned >1 times 800s 12.17% overall alignment rate 800s Flattened IUPAC characters 800s Mutating sequence Sim.pm.2 800s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutating sequence Sim.pm.1 800s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutated reference genome to subject genome 800s SNPs introduced: 3 800s Reference gaps introduced: 0 800s Read gaps introduced: 1 800s Rearrangements introduced: 1 800s Created read sampler 800s Sampling 85 reads 800s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 800s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 800s parsing sequence Sim.pm.1... 800s parsing sequence Sim.pm.2... 800s Parsed 78 reference bases 800s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 800s *** Run 39 of 100 800s /usr/bin/bowtie2 --large-index --cp-min 7 -k 5 --trim5 0 --np 11 --trim3 5 --n-ceil 0.919811005556926,1.32744615028283 --cp-ival 2 --local --mp 8.27081219666593,2.76208877785948 --mm --gbar 1 --rdg 2.43290333021282,14.4440835210248 --score-min L,4.65540985470165,3.18680356670092 --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 800s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 800s 85 reads; of these: 800s 85 (100.00%) were unpaired; of these: 800s 85 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s Read 50 alignments... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s --- Summary --- 800s Read 1 reference strings 800s Checked 0 alignments, 0 edits 800s --------------- 800s PASSED 800s ALSO checking that bowtie2 and bowtie2-align match up 800s /usr/bin/bowtie2 --large-index --cp-min 7 -k 5 --trim5 0 --np 11 --trim3 5 --n-ceil 0.919811005556926,1.32744615028283 --cp-ival 2 --local --mp 8.27081219666593,2.76208877785948 --mm --gbar 1 --rdg 2.43290333021282,14.4440835210248 --score-min L,4.65540985470165,3.18680356670092 --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 800s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_29_29_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_29_29_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_85_85_1/1' because length (0) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_85_85_1/1' because it was < 2 characters long 800s 85 reads; of these: 800s 85 (100.00%) were unpaired; of these: 800s 85 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 800s Flattened IUPAC characters 800s Mutating sequence Sim.pm.1 800s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutating sequence Sim.pm.2 800s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutated reference genome to subject genome 800s SNPs introduced: 10 800s Reference gaps introduced: 1 800s Read gaps introduced: 0 800s Rearrangements introduced: 0 800s Created read sampler 800s Sampling 113 reads 800s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 800s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 800s parsing sequence Sim.pm.1... 800s parsing sequence Sim.pm.2... 800s Parsed 78 reference bases 800s *** Run 40 of 100 800s /usr/bin/bowtie2 --rfg 47.8221353543371 --rdg 21.0665029835202 --score-min L,2.10902509198856,8.78880683847171 --trim3 7 --cp-ival 2 -D 43 --local -M 2 --np 7 -R 2 --large-index --cp-min 6 -r -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw 800s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 800s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '10' because it was < 2 characters long 800s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '13' because it was < 2 characters long 800s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '15' because it was < 2 characters long 800s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '18' because it was < 2 characters long 800s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '19' because it was < 2 characters long 800s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '22' because it was < 2 characters long 800s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '24' because it was < 2 characters long 800s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '26' because it was < 2 characters long 800s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '31' because it was < 2 characters long 800s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '33' because it was < 2 characters long 800s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '34' because it was < 2 characters long 800s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '37' because it was < 2 characters long 800s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '39' because it was < 2 characters long 800s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '40' because it was < 2 characters long 800s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '42' because it was < 2 characters long 800s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '46' because it was < 2 characters long 800s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '50' because it was < 2 characters long 800s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '52' because it was < 2 characters long 800s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '55' because it was < 2 characters long 800s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '59' because it was < 2 characters long 800s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '61' because it was < 2 characters long 800s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '66' because it was < 2 characters long 800s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '72' because it was < 2 characters long 800s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '85' because it was < 2 characters long 800s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '88' because it was < 2 characters long 800s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '92' because it was < 2 characters long 800s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '97' because it was < 2 characters long 800s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '106' because it was < 2 characters long 800s Warning: skipping read '107' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '107' because it was < 2 characters long 800s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '110' because it was < 2 characters long 800s 113 reads; of these: 800s 113 (100.00%) were unpaired; of these: 800s 113 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s Read 50 alignments... 800s Read 100 alignments... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s /usr/bin/bowtie2 --rfg 47.8221353543371 --rdg 21.0665029835202 --score-min L,2.10902509198856,8.78880683847171 --trim3 7 --cp-ival 2 -D 43 --local -M 2 --np 7 -R 2 --large-index --cp-min 6 -r -p 2 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s --- Summary --- 800s Read 1 reference strings 800s Checked 0 alignments, 0 edits 800s --------------- 800s PASSED 800s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 800s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 800s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '10' because it was < 2 characters long 800s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '13' because it was < 2 characters long 800s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '15' because it was < 2 characters long 800s Warning: skipping read '18' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '18' because it was < 2 characters long 800s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '19' because it was < 2 characters long 800s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '22' because it was < 2 characters long 800s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '24' because it was < 2 characters long 800s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '26' because it was < 2 characters long 800s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '31' because it was < 2 characters long 800s Warning: skipping read '33' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '33' because it was < 2 characters long 800s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '34' because it was < 2 characters long 800s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '37' because it was < 2 characters long 800s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '39' because it was < 2 characters long 800s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '40' because it was < 2 characters long 800s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '42' because it was < 2 characters long 800s Warning: skipping read '46' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '46' because it was < 2 characters long 800s Warning: skipping read '50' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '50' because it was < 2 characters long 800s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '52' because it was < 2 characters long 800s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '55' because it was < 2 characters long 800s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '59' because it was < 2 characters long 800s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '61' because it was < 2 characters long 800s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '66' because it was < 2 characters long 800s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '72' because it was < 2 characters long 800s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '85' because it was < 2 characters long 800s Warning: skipping read '88' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '88' because it was < 2 characters long 800s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '92' because it was < 2 characters long 800s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '97' because it was < 2 characters long 800s Warning: skipping read '106' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '106' because it was < 2 characters long 800s Warning: skipping read '107' because length (1) <= # seed mismatches (0) 800s Warning: skipping read '107' because it was < 2 characters long 800s Warning: skipping read '110' because length (0) <= # seed mismatches (0) 800s Warning: skipping read '110' because it was < 2 characters long 800s 113 reads; of these: 800s 113 (100.00%) were unpaired; of these: 800s 113 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 800s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 800s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 800s Flattened IUPAC characters 800s Mutating sequence Sim.pm.1 800s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutating sequence Sim.pm.2 800s Introducing 10 SNPs, 0/1 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutated reference genome to subject genome 800s SNPs introduced: 13 800s Reference gaps introduced: 0 800s Read gaps introduced: 1 800s Rearrangements introduced: 0 800s Created read sampler 800s Sampling 73 reads 800s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 800s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 800s *** Run 41 of 100 800s /usr/bin/bowtie2 --np 4 --cp-min 4 --large-index --mm --gbar 2 --score-min L,8.65662547751012,4.69432880544008 --rdg 32.6986068679865 --trim3 0 --cp-ival 1 --local --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 800s parsing sequence Sim.pm.1... 800s parsing sequence Sim.pm.2... 800s Parsed 78 reference bases 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 800s 73 reads; of these: 800s 73 (100.00%) were unpaired; of these: 800s 73 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s Read 50 alignments... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s /usr/bin/bowtie2 --np 4 --cp-min 4 --large-index --mm --gbar 2 --score-min L,8.65662547751012,4.69432880544008 --rdg 32.6986068679865 --trim3 0 --cp-ival 1 --local --qseq -p 2 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s --- Summary --- 800s Read 1 reference strings 800s Checked 0 alignments, 0 edits 800s --------------- 800s PASSED 800s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 800s 73 reads; of these: 800s 73 (100.00%) were unpaired; of these: 800s 73 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 800s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 800s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 800s /usr/bin/bowtie2 --np 4 --cp-min 4 --large-index --mm --gbar 2 --score-min L,8.65662547751012,4.69432880544008 --rdg 32.6986068679865 --trim3 0 --cp-ival 1 --local --qseq -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 800s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 800s Warning: skipping read 'R_1_1_1_71_71_1/1' because length (1) <= # seed mismatches (0) 800s Warning: skipping read 'R_1_1_1_71_71_1/1' because it was < 2 characters long 800s 73 reads; of these: 800s 73 (100.00%) were unpaired; of these: 800s 73 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 800s Flattened IUPAC characters 800s Mutating sequence Sim.pm.1 800s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutating sequence Sim.pm.2 800s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutated reference genome to subject genome 800s SNPs introduced: 7 800s Reference gaps introduced: 0 800s Read gaps introduced: 0 800s Rearrangements introduced: 0 800s Created read sampler 800s Sampling 52 reads 800s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 800s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 800s parsing sequence Sim.pm.1... 800s parsing sequence Sim.pm.2... 800s Parsed 78 reference bases 800s *** Run 42 of 100 800s /usr/bin/bowtie2 --rfg 9.8642299554588,7.88864524128607 --rdg 7.83850171988488,18.0104582230043 --score-min L,2.1028101326613,9.70420973322253 --cp-ival 1 --local --mp 8.5552774808363,1.61973458886027 -M 2 --trim5 4 --large-index --cp-min 2 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 800s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 800s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '22' because it was < 2 characters long 800s Warning: skipping mate #2 of read '22' because it was < 2 characters long 800s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '27' because it was < 2 characters long 800s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '33' because it was < 2 characters long 800s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '34' because it was < 2 characters long 800s 52 reads; of these: 800s 46 (88.46%) were paired; of these: 800s 46 (100.00%) aligned concordantly 0 times 800s 0 (0.00%) aligned concordantly exactly 1 time 800s 0 (0.00%) aligned concordantly >1 times 800s ---- 800s 46 pairs aligned concordantly 0 times; of these: 800s 0 (0.00%) aligned discordantly 1 time 800s ---- 800s 46 pairs aligned 0 times concordantly or discordantly; of these: 800s 92 mates make up the pairs; of these: 800s 92 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 6 (11.54%) were unpaired; of these: 800s 6 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s Read 50 alignments... 800s Read 100 alignments... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s --- Summary --- 800s Read 1 reference strings 800s Checked 0 alignments, 0 edits 800s --------------- 800s PASSED 800s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 800s /usr/bin/bowtie2 --rfg 9.8642299554588,7.88864524128607 --rdg 7.83850171988488,18.0104582230043 --score-min L,2.1028101326613,9.70420973322253 --cp-ival 1 --local --mp 8.5552774808363,1.61973458886027 -M 2 --trim5 4 --large-index --cp-min 2 -f -p 2 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 800s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 800s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read '22' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '22' because it was < 2 characters long 800s Warning: skipping mate #2 of read '22' because it was < 2 characters long 800s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '27' because it was < 2 characters long 800s Warning: skipping mate #1 of read '33' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '33' because it was < 2 characters long 800s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '34' because it was < 2 characters long 800s 52 reads; of these: 800s 46 (88.46%) were paired; of these: 800s 46 (100.00%) aligned concordantly 0 times 800s 0 (0.00%) aligned concordantly exactly 1 time 800s 0 (0.00%) aligned concordantly >1 times 800s ---- 800s 46 pairs aligned concordantly 0 times; of these: 800s 0 (0.00%) aligned discordantly 1 time 800s ---- 800s 46 pairs aligned 0 times concordantly or discordantly; of these: 800s 92 mates make up the pairs; of these: 800s 92 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 6 (11.54%) were unpaired; of these: 800s 6 (100.00%) aligned 0 times 800s 0 (0.00%) aligned exactly 1 time 800s 0 (0.00%) aligned >1 times 800s 0.00% overall alignment rate 800s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 800s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 800s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 800s Flattened IUPAC characters 800s Mutating sequence Sim.pm.1 800s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutating sequence Sim.pm.2 800s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutated reference genome to subject genome 800s SNPs introduced: 12 800s Reference gaps introduced: 0 800s Read gaps introduced: 1 800s Rearrangements introduced: 0 800s Created read sampler 800s Sampling 96 reads 800s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 800s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 800s parsing sequence Sim.pm.1... 800s parsing sequence Sim.pm.2... 800s Parsed 78 reference bases 800s *** Run 43 of 100 800s /usr/bin/bowtie2 --trim5 1 -R 4 --large-index --cp-min 3 -a --rfg 6.26699078348196,3.26646091167311 --score-min L,3.14102315622706,6.07809449296353 --gbar 4 --mp 5.45369014449588,1.93822639889514 --nofw --cp-ival 1 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 800s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '17' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 800s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read '20' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 800s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read '40' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 800s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '53' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 800s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '55' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 800s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read '80' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 800s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '92' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 800s Warning: skipping mate #1 of read '94' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '94' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 800s Read 50 alignments... 800s 96 reads; of these: 800s 96 (100.00%) were paired; of these: 800s 95 (98.96 Read 100 alignments... 800s %) aligned concordantly 0 times 800s 0 (0.00%) aligned concordantly exactly 1 time 800s 1 (1.04%) aligned concordantly >1 times 800s ---- 800s 95 pairs aligned concordantly 0 times; of these: 800s 0 (0.00%) aligned discordantly 1 time 800s ---- 800s 95 pairs aligned 0 times concordantly or discordantly; of these: 800s 190 mates make up the pairs; of these: 800s 172 (90.53%) aligned 0 times 800s 10 (5.26%) aligned exactly 1 time 800s 8 (4.21%) aligned >1 times 800s 10.42% overall alignment rate 800s Read 150 alignments... 800s Read 200 alignments... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CAC 800s CAC 800s Processing line... 800s CAC 800s CAC 800s Processing line... 800s ATCACATT 800s ATCACATT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s TACCACAATATCAC 800s TACCACAATATCAC 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s ACCCGAA 800s ACCCGAA 800s Processing line... 800s Processing line... 800s TA 800s TA 800s Processing line... 800s TA 800s TA 800s Processing line... 800s TA 800s TA 800s Processing line... 800s TA 800s TA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s AT 800s AT 800s Processing line... 800s AT 800s AT 800s Processing line... 800s AT 800s AT 800s Processing line... 800s AT 800s AT 800s Processing line... 800s AT 800s AT 800s Processing line... 800s AT 800s AT 800s Processing line... 800s AT 800s AT 800s Processing line... 800s Processing line... 800s CA 800s CA 800s Processing line... 800s ACCA 800s ACCA 800s Processing line... 800s CA 800s CA 800s Processing line... 800s ACCA 800s ACCA 800s Processing line... 800s CA 800s CA 800s Processing line... 800s ACCA 800s ACCA 800s Processing line... 800s CA 800s CA 800s Processing line... 800s ACCA 800s ACCA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CACAT 800s CACAT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s ACCCG 800s ACCCG 800s Processing line... 800s Processing line... 800s GT 800s GT 800s Processing line... 800s GT 800s GT 800s Processing line... 800s GT 800s GT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s AATATC 800s AATATC 800s Processing line... 800s Processing line... 800s TAT 800s TAT 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s GACAACCCGA 800s GACAACCCGA 800s Processing line... 800s CACA 800s CACA 800s Processing line... 800s CACA 800s CACA 800s Processing line... 800s Processing line... 800s Processing line... 800s TATC 800s TATC 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s GAA 800s GAA 800s Processing line... 800s GAA 800s GAA 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CCACAATATCAC 800s CCACAATATCAC 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CC 800s CC 800s Processing line... 800s CC 800s CC 800s Processing line... 800s CC 800s CC 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s Processing line... 800s CACA 800s CACA 800s Processing line... 800s CACA 800s CACA 800s Processing line... 800s --- Summary --- 800s Read 1 reference strings 800s Checked 43 alignments, 0 edits 800s --------------- 800s PASSED 800s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 800s /usr/bin/bowtie2 --trim5 1 -R 4 --large-index --cp-min 3 -a --rfg 6.26699078348196,3.26646091167311 --score-min L,3.14102315622706,6.07809449296353 --gbar 4 --mp 5.45369014449588,1.93822639889514 --nofw --cp-ival 1 -f -p 2 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 800s Warning: skipping mate #1 of read '17' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '17' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 800s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read '20' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 800s Warning: skipping mate #2 of read '40' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read '40' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 800s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '53' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 800s Warning: skipping mate #1 of read '55' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '55' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 800s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #2 of read '80' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 800s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '92' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 800s Warning: skipping mate #1 of read '94' because length (1) <= # seed mismatches (0) 800s Warning: skipping mate #1 of read '94' because it was < 2 characters long 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 800s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 800s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 800s 96 reads; of these: 800s 96 (100.00%) were paired; of these: 800s 95 (98.96%) aligned concordantly 0 times 800s 0 (0.00%) aligned concordantly exactly 1 time 800s 1 (1.04%) aligned concordantly >1 times 800s ---- 800s 95 pairs aligned concordantly 0 times; of these: 800s 0 (0.00%) aligned discordantly 1 time 800s ---- 800s 95 pairs aligned 0 times concordantly or discordantly; of these: 800s 190 mates make up the pairs; of these: 800s 172 (90.53%) aligned 0 times 800s 10 (5.26%) aligned exactly 1 time 800s 8 (4.21%) aligned >1 times 800s 10.42% overall alignment rate 800s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 800s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 800s Flattened IUPAC characters 800s Mutating sequence Sim.pm.2 800s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutating sequence Sim.pm.1 800s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 800s Finished SNPs 800s Finished ref gaps 800s Finished read gaps 800s Mutated reference genome to subject genome 800s SNPs introduced: 8 800s Reference gaps introduced: 1 800s Read gaps introduced: 0 800s Rearrangements introduced: 0 800s Created read sampler 800s Sampling 73 reads 800s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 801s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 801s parsing sequence Sim.pm.1... 801s parsing sequence Sim.pm.2... 801s Parsed 78 reference bases 801s *** Run 44 of 100 801s /usr/bin/bowtie2 --score-min L,5.00573431536901,1.00944262081879 --rdg 6.96289760100017,10.5206339146262 --cp-ival 1 --mp 4.36142392676372,3.05107356344408 -N 1 --np 1 --cp-min 11 --large-index -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 801s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '19' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 801s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '28' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 801s Warning: skipping mate #2 of read '36' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #2 of read '36' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 801s Warning: skipping mate #1 of read '41' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '41' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 801s Read 50 alignments... 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 801s Read 100 alignments... 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 801s 73 reads; of these: 801s 73 (100.00%) were paired; of these: 801s 73 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 73 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 73 pairs aligned 0 times concordantly or discordantly; of these: 801s 146 mates make up the pairs; of these: 801s 131 (89.73%) aligned 0 times 801s 8 (5.48%) aligned exactly 1 time 801s 7 (4.79%) aligned >1 times 801s 10.27% overall alignment rate 801s Read 150 alignments... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TATCACA 801s TATCACA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s CTG 801s CTG 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s CA 801s CA 801s Processing line... 801s TTCGTCGTGACAAC 801s TTCGTCGTGACAAC 801s Processing line... 801s CACA 801s CACA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s ATATCAC 801s ATATCAC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TTCGTCGT 801s TTCGTCGT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TT 801s TT 801s Processing line... 801s Processing line... 801s ACCACA 801s ACCACA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TCGTCGTGACAAC 801s TCGTCGTGACAAC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TCA 801s TCA 801s Processing line... 801s Processing line... 801s TACCACAATATCA 801s TACCACAATATCA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s AAC 801s AAC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TAT 801s TAT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s CT 801s CT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s --- Summary --- 801s Read 1 reference strings 801s Checked 15 alignments, 0 edits 801s --------------- 801s PASSED 801s Flattened IUPAC characters 801s Mutating sequence Sim.pm.2 801s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutating sequence Sim.pm.1 801s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutated reference genome to subject genome 801s SNPs introduced: 5 801s Reference gaps introduced: 1 801s Read gaps introduced: 1 801s Rearrangements introduced: 0 801s Created read sampler 801s Sampling 189 reads 801s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 801s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 801s parsing sequence Sim.pm.1... 801s parsing sequence Sim.pm.2... 801s Parsed 78 reference bases 801s *** Run 45 of 100 801s /usr/bin/bowtie2 --score-min L,4.9617772916104,2.57428352526114 --rfg 37.149331264055 --gbar 1 --mm --nofw -N 1 -L26 --mp 8.68574892929227,3.21711611303262 --local --cp-ival 5 --n-ceil 0.940059848085552,0.0856830697893449 --trim3 6 --norc --np 2 --cp-min 4 --large-index -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 801s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '6' because it was < 2 characters long 801s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '8' because it was < 2 characters long 801s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '10' because it was < 2 characters long 801s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #2 of read '14' because it was < 2 characters long 801s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '21' because it was < 2 characters long 801s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '26' because it was < 2 characters long 801s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '38' because it was < 2 characters long 801s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #2 of read '43' because it was < 2 characters long 801s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '46' because it was < 2 characters long 801s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '50' because it was < 2 characters long 801s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '56' because it was < 2 characters long 801s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '61' because it was < 2 characters long 801s Read 50 alignments... 801s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '73' because it was < 2 characters long 801s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '81' because it was < 2 characters long 801s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '86' because it was < 2 characters long 801s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '92' because it was < 2 characters long 801s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '95' because it was < 2 characters long 801s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '101' because it was < 2 characters long 801s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '108' because it was < 2 characters long 801s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '123' because it was < 2 characters long 801s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '129' because it was < 2 characters long 801s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '133' because it was < 2 characters long 801s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '137' because it was < 2 characters long 801s Warning: skipping mate #1 of read '138' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '138' because it was < 2 characters long 801s Read 100 alignments... 801s Read 150 alignments... 801s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '148' because it was < 2 characters long 801s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '150' because it was < 2 characters long 801s Warning: skipping read '172' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '172' because it was < 2 characters long 801s Warning: skipping mate #2 of read '174' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #2 of read '174' because it was < 2 characters long 801s Warning: skipping mate #1 of read '177' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '177' because it was < 2 characters long 801s Warning: skipping mate #1 of read '179' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '179' because it was < 2 characters long 801s Warning: skipping mate #1 of read '182' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '182' because it was < 2 characters long 801s Warning: skipping read '187' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '187' because it was < 2 characters long 801s Read 200 alignments... 801s 189 reads; of these: 801s 164 (86.77%) were paired; of these: 801s 164 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 164 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 164 pairs aligned 0 times concordantly or discordantly; of these: 801s 328 mates make up the pairs; of these: 801s 328 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 25 (13.23%) were unpaired; of these: 801s 25 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 0.00% overall alignment rate 801s Read 250 alignments... 801s Read 300 alignments... 801s Read 350 alignments... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s /usr/bin/bowtie2 --score-min L,4.9617772916104,2.57428352526114 --rfg 37.149331264055 --gbar 1 --mm --nofw -N 1 -L26 --mp 8.68574892929227,3.21711611303262 --local --cp-ival 5 --n-ceil 0.940059848085552,0.0856830697893449 --trim3 6 --norc --np 2 --cp-min 4 --large-index -r -p 3 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s --- Summary --- 801s Read 1 reference strings 801s Checked 0 alignments, 0 edits 801s --------------- 801s PASSED 801s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 801s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '6' because it was < 2 characters long 801s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '8' because it was < 2 characters long 801s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '10' because it was < 2 characters long 801s Warning: skipping mate #2 of read '14' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #2 of read '14' because it was < 2 characters long 801s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '21' because it was < 2 characters long 801s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '26' because it was < 2 characters long 801s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '38' because it was < 2 characters long 801s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #2 of read '43' because it was < 2 characters long 801s Warning: skipping mate #1 of read '46' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '46' because it was < 2 characters long 801s Warning: skipping read '50' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '50' because it was < 2 characters long 801s Warning: skipping mate #1 of read '56' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '56' because it was < 2 characters long 801s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '61' because it was < 2 characters long 801s Warning: skipping mate #1 of read '73' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '73' because it was < 2 characters long 801s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '81' because it was < 2 characters long 801s Warning: skipping mate #1 of read '86' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '86' because it was < 2 characters long 801s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '92' because it was < 2 characters long 801s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '95' because it was < 2 characters long 801s Warning: skipping mate #1 of read '101' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '101' because it was < 2 characters long 801s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '108' because it was < 2 characters long 801s Warning: skipping mate #1 of read '123' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '123' because it was < 2 characters long 801s Warning: skipping mate #1 of read '129' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '129' because it was < 2 characters long 801s Warning: skipping mate #1 of read '133' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '133' because it was < 2 characters long 801s Warning: skipping mate #1 of read '137' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '137' because it was < 2 characters long 801s Warning: skipping mate #1 of read '138' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '138' because it was < 2 characters long 801s Warning: skipping mate #1 of read '148' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '148' because it was < 2 characters long 801s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '150' because it was < 2 characters long 801s Warning: skipping read '172' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '172' because it was < 2 characters long 801s Warning: skipping mate #2 of read '174' because length (1) <= # seed mismatches (1) 801s Warning: skipping mate #2 of read '174' because it was < 2 characters long 801s Warning: skipping mate #1 of read '177' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '177' because it was < 2 characters long 801s Warning: skipping mate #1 of read '179' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '179' because it was < 2 characters long 801s Warning: skipping mate #1 of read '182' because length (0) <= # seed mismatches (1) 801s Warning: skipping mate #1 of read '182' because it was < 2 characters long 801s Warning: skipping read '187' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '187' because it was < 2 characters long 801s 189 reads; of these: 801s 164 (86.77%) were paired; of these: 801s 164 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 164 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 164 pairs aligned 0 times concordantly or discordantly; of these: 801s 328 mates make up the pairs; of these: 801s 328 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 25 (13.23%) were unpaired; of these: 801s 25 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 0.00% overall alignment rate 801s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 801s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 801s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 801s Flattened IUPAC characters 801s Mutating sequence Sim.pm.2 801s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutating sequence Sim.pm.1 801s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutated reference genome to subject genome 801s SNPs introduced: 7 801s Reference gaps introduced: 0 801s Read gaps introduced: 0 801s Rearrangements introduced: 1 801s Created read sampler 801s Sampling 18 reads 801s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 801s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 801s parsing sequence Sim.pm.1... 801s parsing sequence Sim.pm.2... 801s Parsed 78 reference bases 801s *** Run 46 of 100 801s /usr/bin/bowtie2 --large-index --cp-min 4 --np 1 -M 3 -i C,2.24635674429141 -N 1 -L17 --mp 9.77922063657723,7.49583355251041 --nofw --cp-ival 2 -D 19 --trim3 8 --score-min L,1.44964045762058,2.52469335524316 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 801s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 801s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 801s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '1' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 801s Warning: skipping read '2' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '2' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 801s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '4' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 801s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '6' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 801s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '8' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 801s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '12' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 801s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '17' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 801s Warning: skipping read '18' because length (0) <= # seed mismatches (1) 801s Warning: skipping read '18' because it was < 2 characters long 801s 18 reads; of these: 801s 18 (100.00%) were unpaired; of these: 801s 17 (94.44%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 1 (5.56%) aligned >1 times 801s 5.56% overall alignment rate 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TCG 801s TCG 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s --- Summary --- 801s Read 1 reference strings 801s Checked 1 alignments, 0 edits 801s --------------- 801s PASSED 801s Flattened IUPAC characters 801s Mutating sequence Sim.pm.2 801s Introducing 8 SNPs, 3/0 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutating sequence Sim.pm.1 801s Introducing 5 SNPs, 1/1 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutated reference genome to subject genome 801s SNPs introduced: 13 801s Reference gaps introduced: 4 801s Read gaps introduced: 1 801s Rearrangements introduced: 0 801s Created read sampler 801s Sampling 100 reads 801s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 801s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 801s parsing sequence Sim.pm.1... 801s parsing sequence Sim.pm.2... 801s Parsed 78 reference bases 801s *** Run 47 of 100 801s /usr/bin/bowtie2 --score-min L,6.2219512839177,7.74899764063992 --trim3 3 --cp-ival 2 --n-ceil 1.29703725816131,1.2869421920693 --trim5 4 --np 2 --large-index --cp-min 6 --ma 34.0640837216969 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 801s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 801s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 801s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '9' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 801s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '12' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 801s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '14' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 801s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '22' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 801s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '23' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 801s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '34' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 801s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '43' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 801s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '47' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 801s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '57' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 801s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '58' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 801s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '63' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 801s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '65' because it was < 2 characters long 801s Read 50 alignments... 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 801s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '80' because it was < 2 characters long 801s Read 100 alignments... 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 801s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '81' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 801s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '92' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 801s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '96' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 801s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '98' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 801s 100 reads; of these: 801s 83 (83.00%) were paired; of these: 801s 83 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 83 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 83 pairs aligned 0 times concordantly or discordantly; of these: 801s 166 mates make up the pairs; of these: 801s 152 (91.57%) aligned 0 times 801s 6 (3.61%) aligned exactly 1 time 801s 8 (4.82%) aligned >1 times 801s 17 (17.00%) were unpaired; of these: 801s 17 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 7.65% overall alignment rate 801s Read 150 alignments... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s AA 801s AA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TT 801s TT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s AA 801s AA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TGG 801s TGG 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s AA 801s AA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s CCC 801s CCC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s GTCG 801s GTCG 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s CC 801s CC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s AA 801s AA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s CGTCGT 801s CGTCGT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s CA 801s CA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s AATAT 801s AATAT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TGAC 801s TGAC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TTCGTCGTGAC 801s TTCGTCGTGAC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s --- Summary --- 801s Read 1 reference strings 801s Checked 14 alignments, 0 edits 801s --------------- 801s PASSED 801s ALSO checking that bowtie2 and bowtie2-align match up 801s /usr/bin/bowtie2 --score-min L,6.2219512839177,7.74899764063992 --trim3 3 --cp-ival 2 --n-ceil 1.29703725816131,1.2869421920693 --trim5 4 --np 2 --large-index --cp-min 6 --ma 34.0640837216969 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 801s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 801s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 801s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '9' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 801s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '12' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 801s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '14' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 801s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '22' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 801s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '23' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 801s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '34' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 801s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '43' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 801s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '47' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 801s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '57' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 801s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '58' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 801s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '63' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 801s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '65' because it was < 2 characters long 801s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 801s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '80' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 801s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '81' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 801s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '92' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 801s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '96' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 801s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '98' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 801s 100 reads; of these: 801s 83 (83.00%) were paired; of these: 801s 83 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 83 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 83 pairs aligned 0 times concordantly or discordantly; of these: 801s 166 mates make up the pairs; of these: 801s 152 (91.57%) aligned 0 times 801s 6 (3.61%) aligned exactly 1 time 801s 8 (4.82%) aligned >1 times 801s 17 (17.00%) were unpaired; of these: 801s 17 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 7.65% overall alignment rate 801s /usr/bin/bowtie2 --score-min L,6.2219512839177,7.74899764063992 --trim3 3 --cp-ival 2 --n-ceil 1.29703725816131,1.2869421920693 --trim5 4 --np 2 --large-index --cp-min 6 --ma 34.0640837216969 -q -p 3 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 801s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 801s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 801s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 801s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '9' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 801s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '12' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 801s Warning: skipping mate #1 of read '14' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '14' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 801s Warning: skipping mate #1 of read '22' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '22' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 801s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '23' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 801s Warning: skipping mate #1 of read '34' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '34' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 801s Warning: skipping mate #2 of read '43' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '43' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 801s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '47' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 801s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '57' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 801s Warning: skipping mate #2 of read '58' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '58' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 801s Warning: skipping mate #2 of read '63' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '63' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 801s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '65' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 801s Warning: skipping mate #2 of read '80' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '80' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 801s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '81' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 801s Warning: skipping mate #1 of read '92' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '92' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 801s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '96' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 801s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '98' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 801s 100 reads; of these: 801s 83 (83.00%) were paired; of these: 801s 83 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 83 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 83 pairs aligned 0 times concordantly or discordantly; of these: 801s 166 mates make up the pairs; of these: 801s 152 (91.57%) aligned 0 times 801s 6 (3.61%) aligned exactly 1 time 801s 8 (4.82%) aligned >1 times 801s 17 (17.00%) were unpaired; of these: 801s 17 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 7.65% overall alignment rate 801s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 801s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 801s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 801s Flattened IUPAC characters 801s Mutating sequence Sim.pm.1 801s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutating sequence Sim.pm.2 801s Introducing 7 SNPs, 3/0 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutated reference genome to subject genome 801s SNPs introduced: 9 801s Reference gaps introduced: 3 801s Read gaps introduced: 0 801s Rearrangements introduced: 0 801s Created read sampler 801s Sampling 49 reads 801s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 801s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 801s *** Run 48 of 100 801s /usr/bin/bowtie2 --trim3 3 --local --cp-ival 1 --mp 9.4918596101031,6.06602073396173 -N 0 -L20 --mm --score-min L,2.79393418574911,4.42707742392159 --rdg 11.6192379983306 --rfg 21.157893691408,4.81559316410004 --cp-min 4 --large-index -k 4 --trim5 7 --np 4 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 801s parsing sequence Sim.pm.1... 801s parsing sequence Sim.pm.2... 801s Parsed 78 reference bases 801s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '12' because it was < 2 characters long 801s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '19' because it was < 2 characters long 801s Warning: skipping mate #2 of read '19' because it was < 2 characters long 801s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '22' because it was < 2 characters long 801s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '24' because it was < 2 characters long 801s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '40' because it was < 2 characters long 801s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '41' because it was < 2 characters long 801s 49 reads; of these: 801s 42 (85.71%) were paired; of these: 801s 42 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 42 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 42 pairs aligned 0 times concordantly or discordantly; of these: 801s 84 mates make up the pairs; of these: 801s 84 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 7 (14.29%) were unpaired; of these: 801s 7 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 0.00% overall alignment rate 801s Read 50 alignments... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s --- Summary --- 801s Read 1 reference strings 801s Checked 0 alignments, 0 edits 801s --------------- 801s PASSED 801s ALSO checking that bowtie2 and bowtie2-align match up 801s /usr/bin/bowtie2 --trim3 3 --local --cp-ival 1 --mp 9.4918596101031,6.06602073396173 -N 0 -L20 --mm --score-min L,2.79393418574911,4.42707742392159 --rdg 11.6192379983306 --rfg 21.157893691408,4.81559316410004 --cp-min 4 --large-index -k 4 --trim5 7 --np 4 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 801s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '12' because it was < 2 characters long 801s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '19' because it was < 2 characters long 801s Warning: skipping mate #2 of read '19' because it was < 2 characters long 801s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '22' because it was < 2 characters long 801s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '24' because it was < 2 characters long 801s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '40' because it was < 2 characters long 801s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '41' because it was < 2 characters long 801s 49 reads; of these: 801s 42 (85.71%) were paired; of these: 801s 42 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 42 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 42 pairs aligned 0 times concordantly or discordantly; of these: 801s 84 mates make up the pairs; of these: 801s 84 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 7 (14.29%) were unpaired; of these: 801s 7 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 0.00% overall alignment rate 801s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 801s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 801s /usr/bin/bowtie2 --trim3 3 --local --cp-ival 1 --mp 9.4918596101031,6.06602073396173 -N 0 -L20 --mm --score-min L,2.79393418574911,4.42707742392159 --rdg 11.6192379983306 --rfg 21.157893691408,4.81559316410004 --cp-min 4 --large-index -k 4 --trim5 7 --np 4 -r -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 801s Warning: skipping mate #1 of read '12' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '12' because it was < 2 characters long 801s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '19' because it was < 2 characters long 801s Warning: skipping mate #2 of read '19' because it was < 2 characters long 801s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '22' because it was < 2 characters long 801s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '24' because it was < 2 characters long 801s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '40' because it was < 2 characters long 801s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '41' because it was < 2 characters long 801s 49 reads; of these: 801s 42 (85.71%) were paired; of these: 801s 42 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 42 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 42 pairs aligned 0 times concordantly or discordantly; of these: 801s 84 mates make up the pairs; of these: 801s 84 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 7 (14.29%) were unpaired; of these: 801s 7 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 0.00% overall alignment rate 801s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 801s Flattened IUPAC characters 801s Mutating sequence Sim.pm.1 801s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutating sequence Sim.pm.2 801s Introducing 6 SNPs, 0/0 ref/read gaps, and 2 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutated reference genome to subject genome 801s SNPs introduced: 6 801s Reference gaps introduced: 1 801s Read gaps introduced: 1 801s Rearrangements introduced: 2 801s Created read sampler 801s Sampling 145 reads 801s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 801s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 801s parsing sequence Sim.pm.1... 801s parsing sequence Sim.pm.2... 801s Parsed 78 reference bases 801s *** Run 49 of 100 801s /usr/bin/bowtie2 --rdg 9.55747441918837,16.8575525967833 --score-min L,3.98638052020331,2.11089746254789 --mm --mp 5.11704951429237,3.20236237030514 --n-ceil 0.566594132995466,0.197036200318521 --cp-ival 1 --norc --np 2 --large-index --cp-min 3 -R 3 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 801s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 801s Warning: skipping read '5' because length (1) <= # seed mismatches (0) 801s Warning: skipping read '5' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 801s Warning: skipping read '24' because length (1) <= # seed mismatches (0) 801s Warning: skipping read '24' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 801s Warning: skipping read '44' because length (1) <= # seed mismatches (0) 801s Warning: skipping read '44' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 801s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 801s Warning: skipping read '63' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 801s Warning: skipping read '94' because length (1) <= # seed mismatches (0) 801s Warning: skipping read '94' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 801s Warning: skipping read '103' because length (1) <= # seed mismatches (0) 801s Warning: skipping read '103' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '139; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '140; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '141; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '142; setting to 0 instead 801s Warning: skipping read '142' because length (1) <= # seed mismatches (0) 801s Warning: skipping read '142' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '143; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '144; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '145; setting to 0 instead 801s 145 reads; of these: 801s 145 (100.00%) were unpaired; of these: 801s 132 (91.03%) aligned 0 times 801s 6 (4.14%) aligned exactly 1 time 801s 7 (4.83%) aligned >1 times 801s 8.97% overall alignment rate 801s Read 50 alignments... 801s Read 100 alignments... 801s Processing line... 801s Processing line... 801s Processing line... 801s *** Run 50 of 100 801s /usr/bin/bowtie2 --large-index --cp-min 4 --norc --trim5 5 --cp-ival 1 -D 34 --local --rfg 18.6494125971571,4.27909588288663 --rdg 4.09837090566826 --score-min L,8.08954987889703,7.74882740837072 --mm -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TT 801s TT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s AA 801s AA 801s Processing line... 801s Processing line... 801s Processing line... 801s AC 801s AC 801s Processing line... 801s Processing line... 801s ACT 801s ACT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TATCAC 801s TATCAC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TG 801s TG 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TTC 801s TTC 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s ATT 801s ATT 801s Processing line... 801s CTCAACAACTCATTGGAAT 801s CTCAACAACTCATTGGAAT 801s Processing line... 801s ATT 801s ATT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s ATT 801s ATT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s GG 801s GG 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s CCA 801s CCA 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s --- Summary --- 801s Read 1 reference strings 801s Checked 13 alignments, 0 edits 801s --------------- 801s PASSED 801s Flattened IUPAC characters 801s Mutating sequence Sim.pm.2 801s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutating sequence Sim.pm.1 801s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutated reference genome to subject genome 801s SNPs introduced: 4 801s Reference gaps introduced: 0 801s Read gaps introduced: 1 801s Rearrangements introduced: 0 801s Created read sampler 801s Sampling 74 reads 801s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 801s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 801s parsing sequence Sim.pm.1... 801s parsing sequence Sim.pm.2... 801s Parsed 78 reference bases 801s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '12' because it was < 2 characters long 801s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '14' because it was < 2 characters long 801s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '15' because it was < 2 characters long 801s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '17' because it was < 2 characters long 801s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '18' because it was < 2 characters long 801s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '21' because it was < 2 characters long 801s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '38' because it was < 2 characters long 801s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '39' because it was < 2 characters long 801s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '41' because it was < 2 characters long 801s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '55' because it was < 2 characters long 801s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '62' because it was < 2 characters long 801s 74 reads; of these: 801s 64 (86.49%) were paired; of these: 801s 64 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 64 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 64 pairs aligned 0 times concordantly or discordantly; of these: 801s 128 mates make up the pairs; of these: 801s 128 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 10 (13.51%) were unpaired; of these: 801s 10 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 0.00% overall alignment rate 801s Read 50 alignments... 801s Read 100 alignments... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s --- Summary --- 801s Read 1 reference strings 801s Checked 0 alignments, 0 edits 801s --------------- 801s PASSED 801s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 801s /usr/bin/bowtie2 --large-index --cp-min 4 --norc --trim5 5 --cp-ival 1 -D 34 --local --rfg 18.6494125971571,4.27909588288663 --rdg 4.09837090566826 --score-min L,8.08954987889703,7.74882740837072 --mm -f -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 801s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '12' because it was < 2 characters long 801s Warning: skipping mate #1 of read '14' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '14' because it was < 2 characters long 801s Warning: skipping mate #2 of read '15' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '15' because it was < 2 characters long 801s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '17' because it was < 2 characters long 801s Warning: skipping mate #1 of read '18' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '18' because it was < 2 characters long 801s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '21' because it was < 2 characters long 801s Warning: skipping mate #2 of read '38' because length (1) <= # seed mismatches (0) 801s Warning: skipping mate #2 of read '38' because it was < 2 characters long 801s Warning: skipping mate #1 of read '39' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '39' because it was < 2 characters long 801s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '41' because it was < 2 characters long 801s Warning: skipping mate #1 of read '55' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '55' because it was < 2 characters long 801s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 801s Warning: skipping mate #1 of read '62' because it was < 2 characters long 801s 74 reads; of these: 801s 64 (86.49%) were paired; of these: 801s 64 (100.00%) aligned concordantly 0 times 801s 0 (0.00%) aligned concordantly exactly 1 time 801s 0 (0.00%) aligned concordantly >1 times 801s ---- 801s 64 pairs aligned concordantly 0 times; of these: 801s 0 (0.00%) aligned discordantly 1 time 801s ---- 801s 64 pairs aligned 0 times concordantly or discordantly; of these: 801s 128 mates make up the pairs; of these: 801s 128 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 10 (13.51%) were unpaired; of these: 801s 10 (100.00%) aligned 0 times 801s 0 (0.00%) aligned exactly 1 time 801s 0 (0.00%) aligned >1 times 801s 0.00% overall alignment rate 801s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 801s Flattened IUPAC characters 801s Mutating sequence Sim.pm.1 801s Introducing 0 SNPs, 0/1 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutating sequence Sim.pm.2 801s Introducing 3 SNPs, 0/3 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutated reference genome to subject genome 801s SNPs introduced: 3 801s Reference gaps introduced: 0 801s Read gaps introduced: 4 801s Rearrangements introduced: 0 801s Created read sampler 801s Sampling 40 reads 801s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 801s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 801s parsing sequence Sim.pm.1... 801s parsing sequence Sim.pm.2... 801s Parsed 78 reference bases 801s *** Run 51 of 100 801s /usr/bin/bowtie2 --mp 3.7503818035044,1.56528263820756 -N 0 -L12 --cp-ival 5 --n-ceil 1.24322268631027,0.333230764989096 --trim3 9 --rfg 43.5897227456451,7.58075611729374 --rdg 25.4894381317321,5.71211980820176 --score-min L,3.60191878358046,1.55934112171829 --mm -a --large-index --cp-min 2 --np 3 -i S,0.882612220487576,1.2311719919786 -r -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw 801s Warning: minimum score function gave positive number in --end-to-end mode for read '0; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 801s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '3' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 801s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '4' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 801s Warning: skipping read '9' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '9' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 801s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '13' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 801s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '16' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 801s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '17' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 801s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '19' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 801s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '20' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 801s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '22' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 801s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '28' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 801s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '29' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 801s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '31' because it was < 2 characters long 801s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 801s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 801s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 801s Warning: skipping read '39' because it was < 2 characters long 801s 40 reads; of these: 801s 40 (100.00%) were unpaired; of these: 801s 37 (92.50%) aligned 0 times 801s 2 (5.00%) aligned exactly 1 time 801s 1 (2.50%) aligned >1 times 801s 7.50% overall alignment rate 801s Read 50 alignments... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s TGGA 801s TGGA 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s AT 801s AT 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s Processing line... 801s AATATCACAT 801s AATATCACAT 801s Processing line... 801s --- Summary --- 801s Read 1 reference strings 801s Checked 16 alignments, 0 edits 801s --------------- 801s PASSED 801s Flattened IUPAC characters 801s Mutating sequence Sim.pm.2 801s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutating sequence Sim.pm.1 801s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 801s Finished SNPs 801s Finished ref gaps 801s Finished read gaps 801s Mutated reference genome to subject genome 801s SNPs introduced: 6 801s Reference gaps introduced: 0 801s Read gaps introduced: 0 801s Rearrangements introduced: 0 801s Created read sampler 801s Sampling 171 reads 802s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 802s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 802s parsing sequence Sim.pm.1... 802s parsing sequence Sim.pm.2... 802s Parsed 78 reference bases 802s *** Run 52 of 100 802s /usr/bin/bowtie2 --ma 33.9934347581314 --large-index --cp-ival 2 --cp-min 2 --trim3 0 --score-min L,3.62224709144375,5.06170396052526 --trim5 1 -M 2 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 802s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 802s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 802s Warning: skipping mate #2 of read '39' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '39' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 802s Warning: skipping mate #1 of read '49' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '49' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 802s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '60' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 802s Read 50 alignments... 802s Read 100 alignments... 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 802s Warning: skipping mate #1 of read '84' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '84' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 802s Warning: skipping mate #1 of read '108' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '108' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 802s Warning: skipping mate #1 of read '113' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '113' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 802s Read 150 alignments... 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 802s Read 200 alignments... 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 802s 171 reads; of these: 802s 165 (96.49%) were paired; of these: 802s 164 (99.39%) aligned concordantly 0 times 802s 0 (0.00%) aligned concordantly exactly 1 time 802s 1 (0.61%) aligned concordantly >1 times 802s ---- 802s 164 pairs aligned concordantly 0 times; of these: 802s 0 (0.00%) aligned discordantly 1 time 802s ---- 802s 164 pairs aligned 0 times concordantly or discordantly; of these: 802s 328 mates make up the pairs; of these: 802s 298 (90.85%) aligned 0 times 802s 18 (5.49%) aligned exactly 1 time 802s 12 (3.66%) aligned >1 times 802s 6 (3.51%) were unpaired; of these: 802s 5 (83.33%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 1 (16.67%) aligned >1 times 802s 9.82% overall alignment rate 802s Read 250 alignments... 802s Read 300 alignments... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CGTGACAACC 802s CGTGACAACC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TTCGTCGTGAC 802s TTCGTCGTGAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TCGTG 802s TCGTG 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACAATA 802s ACAATA 802s Processing line... 802s Processing line... 802s AT 802s AT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TCGTGACA 802s TCGTGACA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s GTGACAAC 802s GTGACAAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TC 802s TC 802s Processing line... 802s Processing line... 802s *** Run 53 of 100 802s /usr/bin/bowtie2 --mm -k 8 --score-min L,8.27235907695746,5.73189194230866 --np 11 --trim3 3 --mp 6.24616193022754,5.84515208231189 --cp-min 7 --cp-ival 1 --large-index -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AT 802s AT 802s Processing line... 802s TACCACA 802s TACCACA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACATT 802s ACATT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACAATATCACATT 802s ACAATATCACATT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TA 802s TA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TCGTGACAACCCG 802s TCGTGACAACCCG 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AT 802s AT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TCGT 802s TCGT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CGTGACAACCCGA 802s CGTGACAACCCGA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TACCACAA 802s TACCACAA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s GTCG 802s GTCG 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AAC 802s AAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CATT 802s CATT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CAT 802s CAT 802s Processing line... 802s Processing line... 802s TGAC 802s TGAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s GTCGT 802s GTCGT 802s Processing line... 802s Processing line... 802s AT 802s AT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TCGTGACAACCCGAA 802s TCGTGACAACCCGAA 802s Processing line... 802s Processing line... 802s ATC 802s ATC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TCGTGACAACC 802s TCGTGACAACC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TA 802s TA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TGACAA 802s TGACAA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CCC 802s CCC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s --- Summary --- 802s Read 1 reference strings 802s Checked 33 alignments, 0 edits 802s --------------- 802s PASSED 802s Flattened IUPAC characters 802s Mutating sequence Sim.pm.2 802s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutating sequence Sim.pm.1 802s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutated reference genome to subject genome 802s SNPs introduced: 8 802s Reference gaps introduced: 0 802s Read gaps introduced: 1 802s Rearrangements introduced: 1 802s Created read sampler 802s Sampling 63 reads 802s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 802s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 802s parsing sequence Sim.pm.1... 802s parsing sequence Sim.pm.2... 802s Parsed 78 reference bases 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 802s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '2' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 802s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '5' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 802s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '6' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 802s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '11' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 802s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '19' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 802s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '31' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 802s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '62' because it was < 2 characters long 802s 63 reads; of these: 802s 60 (95.24%) were paired; of these: 802s 60 (100.00%) aligned concordantly 0 times 802s 0 (0.00%) aligned concordantly exactly 1 time 802s 0 (0.00%) aligned concordantly >1 times 802s ---- 802s 60 pairs aligned concordantly 0 times; of these: 802s 0 (0.00%) aligned discordantly 1 time 802s ---- 802s 60 pairs aligned 0 times concordantly or discordantly; of these: 802s 120 mates make up the pairs; of these: 802s 102 (85.00%) aligned 0 times 802s 9 (7.50%) aligned exactly 1 time 802s 9 (7.50%) aligned >1 times 802s 3 (4.76%) were unpaired; of these: 802s 2 (66.67%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 1 (33.33%) aligned >1 times 802s 15.45% overall alignment rate 802s Read 50 alignments... 802s Read 100 alignments... 802s Read 150 alignments... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TTAAT 802s TTAAT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AATATC 802s AATATC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TCGTCGTGAC 802s TCGTCGTGAC 802s Processing line... 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s /usr/bin/bowtie2 --mm -k 8 --score-min L,8.27235907695746,5.73189194230866 --np 11 --trim3 3 --mp 6.24616193022754,5.84515208231189 --cp-min 7 --cp-ival 1 --large-index -r -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s TGT 802s TGT 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s TCATTGG 802s TCATTGG 802s Processing line... 802s Processing line... 802s CCACAA 802s CCACAA 802s Processing line... 802s Processing line... 802s CC 802s CC 802s Processing line... 802s CC 802s CC 802s Processing line... 802s CC 802s CC 802s Processing line... 802s GG 802s GG 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CCACAATATCAC 802s CCACAATATCAC 802s Processing line... 802s Processing line... 802s CGT 802s CGT 802s Processing line... 802s CGT 802s CGT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s TC 802s TC 802s Processing line... 802s Processing line... 802s GG 802s GG 802s Processing line... 802s CC 802s CC 802s Processing line... 802s CC 802s CC 802s Processing line... 802s CC 802s CC 802s Processing line... 802s Processing line... 802s CCCGA 802s CCCGA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CACAAT 802s CACAAT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AA 802s AA 802s Processing line... 802s TT 802s TT 802s Processing line... 802s AA 802s AA 802s Processing line... 802s AA 802s AA 802s Processing line... 802s AA 802s AA 802s Processing line... 802s AA 802s AA 802s Processing line... 802s AA 802s AA 802s Processing line... 802s AA 802s AA 802s Processing line... 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s ACA 802s ACA 802s Processing line... 802s TGT 802s TGT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACC 802s ACC 802s Processing line... 802s ACC 802s ACC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CT 802s CT 802s Processing line... 802s CT 802s CT 802s Processing line... 802s CT 802s CT 802s Processing line... 802s CT 802s CT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACAATATCACATT 802s ACAATATCACATT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s --- Summary --- 802s Read 1 reference strings 802s Checked 59 alignments, 0 edits 802s --------------- 802s PASSED 802s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 802s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '2' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 802s Warning: skipping mate #1 of read '5' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '5' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 802s Warning: skipping mate #2 of read '6' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '6' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 802s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '11' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 802s Warning: skipping mate #1 of read '19' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '19' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 802s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '31' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 802s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '62' because it was < 2 characters long 802s 63 reads; of these: 802s 60 (95.24%) were paired; of these: 802s 60 (100.00%) aligned concordantly 0 times 802s 0 (0.00%) aligned concordantly exactly 1 time 802s 0 (0.00%) aligned concordantly >1 times 802s ---- 802s 60 pairs aligned concordantly 0 times; of these: 802s 0 (0.00%) aligned discordantly 1 time 802s ---- 802s 60 pairs aligned 0 times concordantly or discordantly; of these: 802s 120 mates make up the pairs; of these: 802s 102 (85.00%) aligned 0 times 802s 9 (7.50%) aligned exactly 1 time 802s 9 (7.50%) aligned >1 times 802s 3 (4.76%) were unpaired; of these: 802s 2 (66.67%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 1 (33.33%) aligned >1 times 802s 15.45% overall alignment rate 802s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 802s Flattened IUPAC characters 802s Mutating sequence Sim.pm.1 802s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutating sequence Sim.pm.2 802s Introducing 1 SNPs, 0/1 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutated reference genome to subject genome 802s SNPs introduced: 3 802s Reference gaps introduced: 0 802s Read gaps introduced: 1 802s Rearrangements introduced: 0 802s Created read sampler 802s Sampling 99 reads 802s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 802s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 802s parsing sequence Sim.pm.1... 802s parsing sequence Sim.pm.2... 802s Parsed 78 reference bases 802s *** Run 54 of 100 802s /usr/bin/bowtie2 --cp-ival 2 --large-index --cp-min 2 --score-min L,4.08594594584098,9.8215329297028 --gbar 1 --np 3 -i S,2.78488718611906,5.69144912565741 -M 3 --trim5 3 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 802s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 802s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '10' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 802s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '18' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 802s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '27' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 802s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '29' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 802s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '41' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 802s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '43' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 802s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '52' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 802s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '53' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 802s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '59' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 802s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '80' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 802s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '94' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 802s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '97' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 802s Read 50 alignments... 802s Read 100 alignments... 802s 99 reads; of these: 802s 89 (89.90%) were paired; of these: 802s 89 (100.00%) aligned concordantly 0 times 802s 0 (0.00%) aligned concordantly exactly 1 time 802s 0 (0.00%) aligned concordantly >1 times 802s ---- 802s 89 pairs aligned concordantly 0 times; of these: 802s 1 (1.12%) aligned discordantly 1 time 802s ---- 802s 88 pairs aligned 0 times concordantly or discordantly; of these: 802s 176 mates make up the pairs; of these: 802s 155 (88.07%) aligned 0 times 802s 12 (6.82%) aligned exactly 1 time 802s 9 (5.11%) aligned >1 times 802s 10 (10.10%) were unpaired; of these: 802s 9 (90.00%) aligned 0 times 802s 1 (10.00%) aligned exactly 1 time 802s 0 (0.00%) aligned >1 times 802s 12.77% overall alignment rate 802s Read 150 alignments... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TACCACAATATCACAT 802s TACCACAATATCACAT 802s Processing line... 802s Processing line... 802s TCGT 802s TCGT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CGTGACAAC 802s CGTGACAAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s GACAACCC 802s GACAACCC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AC 802s AC 802s Processing line... 802s Processing line... 802s CAA 802s CAA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CGTCGTGACAACCCGAA 802s CGTCGTGACAACCCGAA 802s Processing line... 802s CCACAAT 802s CCACAAT 802s Processing line... 802s CACAT 802s CACAT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACCACAAT 802s ACCACAAT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CAC 802s CAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CACAATATCACAT 802s CACAATATCACAT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CACAATATC 802s CACAATATC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AATC 802s AATC 802s Processing line... 802s Processing line... 802s TCGTGAC 802s TCGTGAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TCGTCGTGACAACCCGA 802s TCGTCGTGACAACCCGA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CAACCCGAAC 802s CAACCCGAAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CAAC 802s CAAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TC 802s TC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CGT 802s CGT 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CCCG 802s CCCG 802s Processing line... 802s Processing line... 802s Processing line... 802s TTC 802s TTC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AAC 802s AAC 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACAATATCACA 802s ACAATATCACA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s --- Summary --- 802s Read 1 reference strings 802s Checked 24 alignments, 0 edits 802s --------------- 802s PASSED 802s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 802s /usr/bin/bowtie2 --cp-ival 2 --large-index --cp-min 2 --score-min L,4.08594594584098,9.8215329297028 --gbar 1 --np 3 -i S,2.78488718611906,5.69144912565741 -M 3 --trim5 3 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 802s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 802s Warning: skipping mate #1 of read '10' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '10' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 802s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '18' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 802s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '27' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 802s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '29' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 802s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '41' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 802s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '43' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 802s Warning: skipping mate #2 of read '52' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '52' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 802s Warning: skipping mate #2 of read '53' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '53' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 802s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '59' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 802s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '80' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 802s Warning: skipping mate #2 of read '94' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read '94' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 802s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read '97' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 802s 99 reads; of these: 802s 89 (89.90%) were paired; of these: 802s 89 (100.00%) aligned concordantly 0 times 802s 0 (0.00%) aligned concordantly exactly 1 time 802s 0 (0.00%) aligned concordantly >1 times 802s ---- 802s 89 pairs aligned concordantly 0 times; of these: 802s 1 (1.12%) aligned discordantly 1 time 802s ---- 802s 88 pairs aligned 0 times concordantly or discordantly; of these: 802s 176 mates make up the pairs; of these: 802s 155 (88.07%) aligned 0 times 802s 12 (6.82%) aligned exactly 1 time 802s 9 (5.11%) aligned >1 times 802s 10 (10.10%) were unpaired; of these: 802s 9 (90.00%) aligned 0 times 802s 1 (10.00%) aligned exactly 1 time 802s 0 (0.00%) aligned >1 times 802s 12.77% overall alignment rate 802s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 802s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 802s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 802s Flattened IUPAC characters 802s Mutating sequence Sim.pm.1 802s Introducing 4 SNPs, 1/0 ref/read gaps, and 1 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutating sequence Sim.pm.2 802s Introducing 2 SNPs, 0/2 ref/read gaps, and 1 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutated reference genome to subject genome 802s SNPs introduced: 6 802s Reference gaps introduced: 1 802s Read gaps introduced: 2 802s Rearrangements introduced: 2 802s Created read sampler 802s Sampling 151 reads 802s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 802s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 802s parsing sequence Sim.pm.1... 802s parsing sequence Sim.pm.2... 802s Parsed 78 reference bases 802s *** Run 55 of 100 802s /usr/bin/bowtie2 --mm --rdg 41.7963048204248,11.0641153661766 --score-min L,7.70488319216067,1.61502741662661 --cp-ival 1 --local --nofw -i L,0.262674883160445 --np 2 --large-index --cp-min 2 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 802s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 802s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 802s Read 50 alignments... 802s Read 100 alignments... 802s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 802s Warning: skipping mate #2 of read 'R_1_1_1_91_91_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read 'R_1_1_1_91_91_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_149_149_1/1' because it was < 2 characters long 802s Read 150 alignments... 802s Read 200 alignments... 802s 151 reads; of these: 802s 151 (100.00%) were paired; of these: 802s 151 (100.00%) aligned concordantly 0 times 802s 0 (0.00%) aligned concordantly exactly 1 time 802s 0 (0.00%) aligned concordantly >1 times 802s ---- 802s 151 pairs aligned concordantly 0 times; of these: 802s 0 (0.00%) aligned discordantly 1 time 802s ---- 802s 151 pairs aligned 0 times concordantly or discordantly; of these: 802s 302 mates make up the pairs; of these: 802s 302 (100.00%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 0 (0.00%) aligned >1 times 802s 0.00% overall alignment rate 802s Read 250 alignments... 802s Read 300 alignments... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s --- Summary --- 802s Read 1 reference strings 802s Checked 0 alignments, 0 edits 802s --------------- 802s PASSED 802s Flattened IUPAC characters 802s Mutating sequence Sim.pm.2 802s Introducing 3 SNPs, 1/1 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutating sequence Sim.pm.1 802s Introducing 4 SNPs, 0/0 ref/read ga*** Run 56 of 100 802s /usr/bin/bowtie2 --trim3 4 --nofw --cp-ival 1 --local --mm --rfg 9.36854216145635 --rdg 32.0164032021511 --score-min L,4.45499912447991,6.88262956869952 -R 2 --large-index --cp-min 4 --trim5 1 -M 3 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 802s ps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutated reference genome to subject genome 802s SNPs introduced: 7 802s Reference gaps introduced: 1 802s Read gaps introduced: 1 802s Rearrangements introduced: 0 802s Created read sampler 802s Sampling 71 reads 802s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 802s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 802s parsing sequence Sim.pm.1... 802s parsing sequence Sim.pm.2... 802s Parsed 78 reference bases 802s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 802s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 802s Warning: skipping mate #2 of read 'R_1_1_1_23_23_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 802s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 802s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 802s Read 50 alignments... 802s Read 100 alignments... 802s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (0) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 802s 71 reads; of these: 802s 61 (85.92%) were paired; of these: 802s 61 (100.00%) aligned concordantly 0 times 802s 0 (0.00%) aligned concordantly exactly 1 time 802s 0 (0.00%) aligned concordantly >1 times 802s ---- 802s 61 pairs aligned concordantly 0 times; of these: 802s 0 (0.00%) aligned discordantly 1 time 802s ---- 802s 61 pairs aligned 0 times concordantly or discordantly; of these: 802s 122 mates make up the pairs; of these: 802s 122 (100.00%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 0 (0.00%) aligned >1 times 802s 10 (14.08%) were unpaired; of these: 802s 10 (100.00%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 0 (0.00%) aligned >1 times 802s 0.00% overall alignment rate 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s --- Summary --- 802s Read 1 reference strings 802s Checked 0 alignments, 0 edits 802s --------------- 802s PASSED 802s Flattened IUPAC characters 802s Mutating sequence Sim.pm.1 802s Introducing 1 SNPs, 0/0 ref/read gaps, and 1 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutating sequence Sim.pm.2 802s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutated reference genome to subject genome 802s SNPs introduced: 4 802s Reference gaps introduced: 1 802s Read gaps introduced: 0 802s Rearrangements introduced: 1 802s Created read sampler 802s Sampling 93 reads 802s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 802s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 802s parsing sequence Sim.pm.1... 802s parsing sequence Sim.pm.2... 802s Parsed 78 reference bases 802s *** Run 57 of 100 802s /usr/bin/bowtie2 --n-ceil 0.719899358316998,1.0567221740826 --cp-ival 2 --local -a --mm --score-min L,7.07300283536559,9.35010798450521 --cp-min 2 --large-index -i S --np 3 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 802s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 802s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #2 of read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 802s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (1) <= # seed mismatches (0) 802s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 802s Read 50 alignments... 802s Read 100 alignments... 802s 93 reads; of these: 802s 93 (100.00%) were paired; of these: 802s 93 (100.00%) aligned concordantly 0 times 802s 0 (0.00%) aligned concordantly exactly 1 time 802s 0 (0.00%) aligned concordantly >1 times 802s ---- 802s 93 pairs aligned concordantly 0 times; of these: 802s 0 (0.00%) aligned discordantly 1 time 802s ---- 802s 93 pairs aligned 0 times concordantly or discordantly; of these: 802s 186 mates make up the pairs; of these: 802s 186 (100.00%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 0 (0.00%) aligned >1 times 802s 0.00% overall alignment rate 802s Read 150 alignments... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s --- Summary --- 802s Read 1 reference strings 802s Checked 0 alignments, 0 edits 802s --------------- 802s PASSED 802s Flattened IUPAC characters 802s Mutating sequence Sim.pm.2 802s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutating sequence Sim.pm.1 802s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutated reference genome to subject genome 802s SNPs introduced: 1 802s Reference gaps introduced: 2 802s Read gaps introduced: 1 802s Rearrangements introduced: 0 802s Created read sampler 802s Sampling 139 reads 802s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 802s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 802s parsing sequence Sim.pm.1... 802s parsing sequence Sim.pm.2... 802s Parsed 78 reference bases 802s *** Run 58 of 100 802s /usr/bin/bowtie2 --large-index --cp-min 2 --trim5 0 --np 1 --trim3 1 --mp 5.44720911421477,3.49461229287183 --cp-ival 1 --local --rfg 28.5971127654214,11.2133430569126 --score-min L,3.64914567590569,5.07254459483842 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 802s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '2' because it was < 2 characters long 802s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '5' because it was < 2 characters long 802s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '10' because it was < 2 characters long 802s Warning: skipping read '73' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '73' because it was < 2 characters long 802s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '88' because it was < 2 characters long 802s Warning: skipping read '106' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '106' because it was < 2 characters long 802s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '109' because it was < 2 characters long 802s Warning: skipping read '117' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '117' because it was < 2 characters long 802s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '121' because it was < 2 characters long 802s Warning: skipping read '122' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '122' because it was < 2 characters long 802s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '124' because it was < 2 characters long 802s 139 reads; of these: 802s 139 (100.00%) were unpaired; of these: 802s 139 (100.00%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 0 (0.00%) aligned >1 times 802s 0.00% overall alignment rate 802s Read 50 alignments... 802s Read 100 alignments... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s --- Summary --- 802s Read 1 reference strings 802s Checked 0 alignments, 0 edits 802s --------------- 802s PASSED 802s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 802s /usr/bin/bowtie2 --large-index --cp-min 2 --trim5 0 --np 1 --trim3 1 --mp 5.44720911421477,3.49461229287183 --cp-ival 1 --local --rfg 28.5971127654214,11.2133430569126 --score-min L,3.64914567590569,5.07254459483842 -q -p 3 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 802s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '2' because it was < 2 characters long 802s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '5' because it was < 2 characters long 802s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '10' because it was < 2 characters long 802s Warning: skipping read '73' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '73' because it was < 2 characters long 802s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '88' because it was < 2 characters long 802s Warning: skipping read '106' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '106' because it was < 2 characters long 802s Warning: skipping read '109' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '109' because it was < 2 characters long 802s Warning: skipping read '117' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '117' because it was < 2 characters long 802s Warning: skipping read '121' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '121' because it was < 2 characters long 802s Warning: skipping read '122' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '122' because it was < 2 characters long 802s Warning: skipping read '124' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '124' because it was < 2 characters long 802s 139 reads; of these: 802s 139 (100.00%) were unpaired; of these: 802s 139 (100.00%) aligned 0 times 802s 0 (0.00%) aligned exactly 1 time 802s 0 (0.00%) aligned >1 times 802s 0.00% overall alignment rate 802s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 802s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 802s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 802s Flattened IUPAC characters 802s Mutating sequence Sim.pm.2 802s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutating sequence Sim.pm.1 802s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 802s Finished SNPs 802s Finished ref gaps 802s Finished read gaps 802s Mutated reference genome to subject genome 802s SNPs introduced: 6 802s Reference gaps introduced: 1 802s Read gaps introduced: 0 802s Rearrangements introduced: 0 802s Created read sampler 802s Sampling 90 reads 802s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 802s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 802s parsing sequence Sim.pm.1... 802s *** Run 59 of 100 802s /usr/bin/bowtie2 --mm --score-min L,5.52695776698711,7.43268392690371 --rfg 42.6397585782127 --rdg 35.5608677951031 --trim3 5 --cp-ival 1 --mp 4.34978002111023,1.75511625278037 --trim5 8 -M 4 --cp-min 10 --large-index --ma 38.3675421039765 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 802s parsing sequence Sim.pm.2... 802s Parsed 78 reference bases 802s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 802s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 802s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 802s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '4' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 802s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '6' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 802s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '7' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 802s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '10' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 802s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '12' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 802s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '13' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 802s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '19' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 802s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '20' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 802s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '29' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 802s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '32' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 802s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '37' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 802s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '39' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 802s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '42' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 802s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '43' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 802s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '44' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 802s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '47' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 802s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '48' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 802s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '50' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 802s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '52' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 802s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '54' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 802s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '59' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 802s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '66' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 802s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '69' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 802s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '71' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 802s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '74' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 802s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '75' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 802s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '76' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 802s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '78' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 802s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '80' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 802s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '82' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 802s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '84' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 802s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '87' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 802s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '90' because it was < 2 characters long 802s 90 reads; of these: 802s 90 (100.00%) were unpaired; of these: 802s 79 (87.78%) aligned 0 times 802s 7 (7.78%) aligned exactly 1 time 802s 4 (4.44%) aligned >1 times 802s 12.22% overall alignment rate 802s Read 50 alignments... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AACA 802s AACA 802s Processing line... 802s Processing line... 802s Processing line... 802s CAACCCG 802s CAACCCG 802s Processing line... 802s CAACCCG 802s CAACCCG 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CT 802s CT 802s Processing line... 802s Processing line... 802s ATA 802s ATA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CAACAACTCATTGGAATA 802s CAACAACTCATTGGAATA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s ACAACCCGAAC 802s ACAACCCGAAC 802s Processing line... 802s TTCGTCGTGACAACCCG 802s TTCGTCGTGACAACCCG 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s TGG 802s TGG 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s CA 802s CA 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s Processing line... 802s AACAA 802s AACAA 802s Processing line... 802s --- Summary --- 802s Read 1 reference strings 802s Checked 11 alignments, 0 edits 802s --------------- 802s PASSED 802s ALSO checking that bowtie2 and bowtie2-align match up 802s /usr/bin/bowtie2 --mm --score-min L,5.52695776698711,7.43268392690371 --rfg 42.6397585782127 --rdg 35.5608677951031 --trim3 5 --cp-ival 1 --mp 4.34978002111023,1.75511625278037 --trim5 8 -M 4 --cp-min 10 --large-index --ma 38.3675421039765 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 802s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 802s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 802s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 802s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '4' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 802s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '6' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 802s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '7' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 802s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '10' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 802s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '12' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 802s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '13' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 802s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '19' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 802s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '20' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 802s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '29' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 802s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '32' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 802s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '37' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 802s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '39' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 802s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '42' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 802s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '43' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 802s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '44' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 802s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '47' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 802s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '48' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 802s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '50' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 802s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '52' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 802s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '54' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 802s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '59' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 802s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '66' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 802s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '69' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 802s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '71' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 802s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '74' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 802s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '75' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 802s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '76' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 802s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '78' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 802s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '80' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 802s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '82' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 802s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '84' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 802s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '87' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 802s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '90' because it was < 2 characters long 802s 90 reads; of these: 802s 90 (100.00%) were unpaired; of these: 802s 79 (87.78%) aligned 0 times 802s 7 (7.78%) aligned exactly 1 time 802s 4 (4.44%) aligned >1 times 802s 12.22% overall alignment rate 802s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 802s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 802s /usr/bin/bowtie2 --mm --score-min L,5.52695776698711,7.43268392690371 --rfg 42.6397585782127 --rdg 35.5608677951031 --trim3 5 --cp-ival 1 --mp 4.34978002111023,1.75511625278037 --trim5 8 -M 4 --cp-min 10 --large-index --ma 38.3675421039765 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 802s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 802s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 802s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 802s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '4' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 802s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '6' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 802s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '7' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 802s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '10' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 802s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '12' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 802s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '13' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 802s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '19' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 802s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '20' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 802s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '29' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 802s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '32' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 802s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '37' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 802s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '39' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 802s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '42' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 802s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '43' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 802s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '44' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 802s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '47' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 802s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '48' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 802s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '50' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 802s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 802s Warning: skipping read '52' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 802s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '54' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 802s Warning: skipping read '59' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '59' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 802s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '66' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 802s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '69' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 802s Warning: skipping read '71' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '71' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 802s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '74' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 802s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '75' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 802s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '76' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 802s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '78' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 802s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '80' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 802s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '82' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 802s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '84' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 802s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '87' because it was < 2 characters long 802s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 802s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 802s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 802s Warning: skipping read '90' because it was < 2 characters long 802s 90 reads; of these: 802s 90 (100.00%) were unpaired; of these: 802s 79 (87.78%) aligned 0 times 802s 7 (7.78%) aligned exactly 1 time 802s 4 (4.44%) aligned >1 times 802s 12.22% overall alignment rate 803s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 803s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 803s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 803s Flattened IUPAC characters 803s Mutating sequence Sim.pm.2 803s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutating sequence Sim.pm.1 803s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutated reference genome to subject genome 803s SNPs introduced: 5 803s Reference gaps introduced: 1 803s Read gaps introduced: 0 803s Rearrangements introduced: 0 803s Created read sampler 803s Sampling 85 reads 803s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 803s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 803s parsing sequence Sim.pm.1... 803s parsing sequence Sim.pm.2... 803s Parsed 78 reference bases 803s *** Run 60 of 100 803s /usr/bin/bowtie2 --trim3 1 --cp-ival 1 --mm --score-min L,2.43172953775945,5.21213533218554 --rdg 34.2544303828043,10.2190355507741 -R 3 --cp-min 3 --large-index -M 2 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 803s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 803s Warning: skipping mate #2 of read '9' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read '9' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 803s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '43' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 803s Warning: skipping mate #1 of read '56' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '56' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 803s Warning: skipping mate #2 of read '84' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read '84' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 803s Read 50 alignments... 803s Read 100 alignments... 803s 85 reads; of these: 803s 84 (98.82%) were paired; of these: 803s 84 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 84 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 84 pairs aligned 0 times concordantly or discordantly; of these: 803s 168 mates make up the pairs; of these: 803s 157 (93.45%) aligned 0 times 803s 6 (3.57%) aligned exactly 1 time 803s 5 (2.98%) aligned >1 times 803s 1 (1.18%) were unpaired; of these: 803s 1 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 6.51% overall alignment rate 803s Read 150 alignments... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TACCA 803s TACCA 803s Processing line... 803s Processing line... 803s CA 803s CA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TGACAACCCGAAC 803s TGACAACCCGAAC 803s Processing line... 803s Processing line... 803s TATCACAT 803s TATCACAT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GACAACC 803s GACAACC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TCG 803s TCG 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GG 803s GG 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s ATC 803s ATC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TATCACA 803s TATCACA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GTCGTGACAACCCGAA 803s GTCGTGACAACCCGAA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s --- Summary --- 803s Read 1 reference strings 803s Checked 11 alignments, 0 edits 803s --------------- 803s PASSED 803s Flattened IUPAC characters 803s Mutating sequence Sim.pm.1 803s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutating sequence Sim.pm.2 803s Introducing 0 SNPs, 1/0 ref/read gaps, and 2 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutated reference genome to subject genome 803s SNPs introduced: 2 803s Reference gaps introduced: 1 803s Read gaps introduced: 1 803s Rearrangements introduced: 3 803s Created read sampler 803s Sampling 25 reads 803s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 803s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 803s parsing sequence Sim.pm.1... 803s parsing sequence Sim.pm.2... 803s Parsed 78 reference bases 803s *** Run 61 of 100 803s /usr/bin/bowtie2 -N 1 --cp-ival 1 -D 7 --trim3 8 --rdg 12.5476499868325 --score-min L,4.23962274443728,1.35871046292148 --ma 27.4400143951183 --large-index --cp-min 2 --norc --trim5 1 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 803s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 803s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '4' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 803s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 803s Warning: skipping read '5' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 803s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '6' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 803s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '15' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 803s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '17' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 803s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '21' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 803s 25 reads; of these: 803s 21 (84.00%) were paired; of these: 803s 21 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 21 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 21 pairs aligned 0 times concordantly or discordantly; of these: 803s 42 mates make up the pairs; of these: 803s 39 (92.86%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 3 (7.14%) aligned >1 times 803s 4 (16.00%) were unpaired; of these: 803s 4 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 6.52% overall alignment rate 803s Read 50 alignments... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TT 803s TT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s /usr/bin/bowtie2 -N 1 --cp-ival 1 -D 7 --trim3 8 --rdg 12.5476499868325 --score-min L,4.23962274443728,1.35871046292148 --ma 27.4400143951183 --large-index --cp-min 2 --norc --trim5 1 -r -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GT 803s GT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TG 803s TG 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s --- Summary --- 803s Read 1 reference strings 803s Checked 3 alignments, 0 edits 803s --------------- 803s PASSED 803s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 803s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 803s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '4' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 803s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 803s Warning: skipping read '5' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 803s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '6' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 803s Warning: skipping mate #1 of read '15' because length (1) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '15' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 803s Warning: skipping mate #1 of read '17' because length (0) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '17' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 803s Warning: skipping mate #1 of read '21' because length (0) <= # seed mismatches (1) 803s Warning: skipping mate #1 of read '21' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 803s 25 reads; of these: 803s 21 (84.00%) were paired; of these: 803s 21 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 21 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 21 pairs aligned 0 times concordantly or discordantly; of these: 803s 42 mates make up the pairs; of these: 803s 39 (92.86%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 3 (7.14%) aligned >1 times 803s 4 (16.00%) were unpaired; of these: 803s 4 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 6.52% overall alignment rate 803s Flattened IUPAC characters 803s Mutating sequence Sim.pm.2 803s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 803s Finished read gaps 803s Mutating sequence Sim.pm.1 803s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutated reference genome to subject genome 803s SNPs introduced: 7 803s Reference gaps introduced: 0 803s Read gaps introduced: 0 803s Rearrangements introduced: 3 803s Created read sampler 803s Sampling 205 reads 803s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 803s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 803s parsing sequence Sim.pm.1... 803s parsing sequence Sim.pm.2... 803s Parsed 78 reference bases 803s *** Run 62 of 100 803s /usr/bin/bowtie2 -i S,1.72166908501735 --norc --np 4 --ma 21.3243515251995 --cp-min 4 --large-index -a --mm --score-min L,2.46567705580152,7.38497536430271 --rdg 19.2901102870979 --rfg 16.443418199518,5.56691698971574 --mp 2.53526123822537,2.15389569712856 --cp-ival 2 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 803s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 803s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read '18' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 803s Read 50 alignments... 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 803s Read 100 alignments... 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 803s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read '110' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 803s Warning: skipping mate #1 of read '130' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '130' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 803s Warning: skipping mate #1 of read '132' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '132' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 803s Warning: skipping mate #1 of read '142' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '142' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 803s Read 150 alignments... 803s Read 200 alignments... 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 803s Warning: skipping mate #1 of read '185' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '185' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '201; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '201; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 803s Read 250 alignments... 803s Read 300 alignments... 803s 205 reads; of these: 803s 205 (100.00%) were paired; of these: 803s 203 (99.02%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 2 (0.98%) aligned concordantly >1 times 803s ---- 803s 203 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 203 pairs aligned 0 times concordantly or discordantly; of these: 803s 406 mates make up the pairs; of these: 803s 385 (94.83%) aligned 0 times 803s 9 (2.22%) aligned exactly 1 time 803s 12 (2.96%) aligned >1 times 803s 6.10% overall alignment rate 803s Read 350 alignments... 803s Read 400 alignments... 803s Read 450 alignments... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TC 803s TC 803s Processing line... 803s TC 803s TC 803s Processing line... 803s TC 803s TC 803s Processing line... 803s TC 803s TC 803s Processing line... 803s TC 803s TC 803s Processing line... 803s TC 803s TC 803s Processing line... 803s TC 803s TC 803s Processing line... 803s TC 803s TC 803s Processing line... 803s TC 803s TC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s Processing line... 803s GG 803s GG 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s AT 803s AT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CG 803s CG 803s Processing line... 803s CG 803s CG 803s Processing line... 803s CG 803s CG 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GG 803s GG 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GACA 803s GACA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CACA 803s CACA 803s Processing line... 803s CACA 803s CACA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GAAT 803s GAAT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TT 803s TT 803s Processing line... 803s TGA 803s TGA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TGACA 803s TGACA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s AC 803s AC 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s AC 803s AC 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s AC 803s AC 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s AC 803s AC 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s AC 803s AC 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s AC 803s AC 803s Processing line... 803s ACA 803s ACA 803s Processing line... 803s AC 803s AC 803s Processing line... 803s AA 803s AA 803s Processing line... 803s AA 803s AA 803s Processing line... 803s AA 803s AA 803s Processing line... 803s AA 803s AA 803s Processing line... 803s AA 803s AA 803s Processing line... 803s AA 803s AA 803s Processing line... 803s AA 803s AA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s ACAAC 803s ACAAC 803s Processing line... 803s ACAAC 803s ACAAC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CACAT 803s CACAT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GTGACA 803s GTGACA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TGT 803s TGT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GA 803s GA 803s Processing line... 803s GA 803s GA 803s Processing line... 803s GA 803s GA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s ATC 803s ATC 803s Processing line... 803s ATC 803s ATC 803s Processing line... 803s ATC 803s ATC 803s Processing line... 803s Processing line... 803s AAC 803s AAC 803s Processing line... 803s AAC 803s AAC 803s Processing line... 803s AAC 803s AAC 803s Processing line... 803s AAC 803s AAC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CGTGAC 803s CGTGAC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CA 803s CA 803s Processing line... 803s CA 803s CA 803s Processing line... 803s CA 803s CA 803s Processing line... 803s CA 803s CA 803s Processing line... 803s CA 803s CA 803s Processing line... 803s CA 803s CA 803s Processing line... 803s CA 803s CA 803s Processing line... 803s CA 803s CA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s --- Summary --- 803s Read 1 reference strings 803s Checked 84 alignments, 0 edits 803s --------------- 803s PASSED 803s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 803s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 803s /usr/bin/bowtie2 -i S,1.72166908501735 --norc --np 4 --ma 21.3243515251995 --cp-min 4 --large-index -a --mm --score-min L,2.46567705580152,7.38497536430271 --rdg 19.2901102870979 --rfg 16.443418199518,5.56691698971574 --mp 2.53526123822537,2.15389569712856 --cp-ival 2 -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 803s Warning: skipping mate #2 of read '18' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read '18' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 803s Warning: skipping mate #2 of read '110' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read '110' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 803s Warning: skipping mate #1 of read '130' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '130' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 803s Warning: skipping mate #1 of read '132' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '132' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 803s Warning: skipping mate #1 of read '142' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '142' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 803s Warning: minimum score function gave positive number in diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 803s *** Run 63 of 100 803s /usr/bin/bowtie2 --trim3 2 --mp 9.77282324931118,2.77098792862798 --cp-ival 2 -D 3 --mm --score-min L,8.96302312699005,8.22531425634013 --ma 24.8254212891501 --cp-min 6 --large-index -i L,0.0969854145048933 --norc --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 803s --end-to-end mode for mate #1 of read '181; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 803s Warning: skipping mate #1 of read '185' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read '185' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '201; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '201; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '204; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '204; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 803s 205 reads; of these: 803s 205 (100.00%) were paired; of these: 803s 203 (99.02%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 2 (0.98%) aligned concordantly >1 times 803s ---- 803s 203 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 203 pairs aligned 0 times concordantly or discordantly; of these: 803s 406 mates make up the pairs; of these: 803s 385 (94.83%) aligned 0 times 803s 9 (2.22%) aligned exactly 1 time 803s 12 (2.96%) aligned >1 times 803s 6.10% overall alignment rate 803s Flattened IUPAC characters 803s Mutating sequence Sim.pm.2 803s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutating sequence Sim.pm.1 803s Introducing 3 SNPs, 0/0 ref/read gaps, and 0 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutated reference genome to subject genome 803s SNPs introduced: 10 803s Reference gaps introduced: 0 803s Read gaps introduced: 0 803s Rearrangements introduced: 1 803s Created read sampler 803s Sampling 89 reads 803s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 803s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 803s parsing sequence Sim.pm.1... 803s parsing sequence Sim.pm.2... 803s Parsed 78 reference bases 803s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 803s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 803s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 803s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 803s Read 50 alignments... 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 803s Read 100 alignments... 803s 89 reads; of these: 803s 86 (96.63%) were paired; of these: 803s 86 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 86 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 86 pairs aligned 0 times concordantly or discordantly; of these: 803s 172 mates make up the pairs; of these: 803s 159 (92.44%) aligned 0 times 803s 6 (3.49%) aligned exactly 1 time 803s 7 (4.07%) aligned >1 times 803s 3 (3.37%) were unpaired; of these: 803s 3 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 7.43% overall alignment rate 803s Read 150 alignments... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CC 803s CC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GTG 803s GTG 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TT 803s TT 803s Processing line... 803s Processing line... 803s /usr/bin/bowtie2 --trim3 2 --mp 9.77282324931118,2.77098792862798 --cp-ival 2 -D 3 --mm --score-min L,8.96302312699005,8.22531425634013 --ma 24.8254212891501 --cp-min 6 --large-index -i L,0.0969854145048933 --norc --qseq -p 3 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 803s AA 803s AA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GTGACAACC 803s GTGACAACC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TCA 803s TCA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CG 803s CG 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CGTCGTGACAAC 803s CGTCGTGACAAC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GTGACAACC 803s GTGACAACC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TCGTGACAACCCGAAC 803s TCGTGACAACCCGAAC 803s Processing line... 803s Processing line... 803s ACAA 803s ACAA 803s Processing line... 803s Processing line... 803s TGT 803s TGT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CC 803s CC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s --- Summary --- 803s Read 1 reference strings 803s Checked 13 alignments, 0 edits 803s --------------- 803s PASSED 803s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 803s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 803s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 803s Warning: skipping read 'R_1_1_1_43_43_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping read 'R_1_1_1_43_43_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 803s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 803s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 803s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_66_66_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 803s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 803s 89 reads; of these: 803s 86 (96.63%) were paired; of these: 803s 86 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 86 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 86 pairs aligned 0 times concordantly or discordantly; of these: 803s 172 mates make up the pairs; of these: 803s 159 (92.44%) aligned 0 times 803s 6 (3.49%) aligned exactly 1 time 803s 7 (4.07%) aligned >1 times 803s 3 (3.37%) were unpaired; of these: 803s 3 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 7.43% overall alignment rate 803s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 803s Flattened IUPAC characters 803s Mutating sequence Sim.pm.1 803s Introducing 2 SNPs, 0/0 ref/read gaps, and 1 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutating sequence Sim.pm.2 803s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutated reference genome to subject genome 803s SNPs introduced: 2 803s Reference gaps introduced: 1 803s Read gaps introduced: 0 803s Rearrangements introduced: 1 803s Created read sampler 803s Sampling 77 reads 803s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 803s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 803s parsing sequence Sim.pm.1... 803s *** Run 64 of 100 803s /usr/bin/bowtie2 --trim5 7 -M 4 --cp-min 4 --large-index --ma 6.43525389162664 --gbar 2 --score-min L,8.23459066401245,7.05934578508343 --rdg 25.1526038264722,13.5542702586916 --rfg 45.3373250121589 --cp-ival 1 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 803s parsing sequence Sim.pm.2... 803s Parsed 78 reference bases 803s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 803s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 803s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 803s Warning: skipping read '1' because length (1) <= # seed mismatches (0) 803s Warning: skipping read '1' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 803s Warning: skipping read '3' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '3' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 803s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 803s Warning: skipping read '4' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 803s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '6' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 803s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '7' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 803s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '15' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 803s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '24' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 803s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '26' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 803s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '29' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 803s Warning: skipping read '30' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '30' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 803s Warning: skipping read '31' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '31' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 803s Warning: skipping read '34' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '34' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 803s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '35' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 803s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '36' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 803s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '38' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 803s Warning: skipping read '40' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '40' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 803s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '43' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 803s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '45' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 803s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 803s Warning: skipping read '55' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 803s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '56' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 803s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '57' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 803s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 803s Warning: skipping read '62' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 803s Warning: skipping read '67' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '67' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 803s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '68' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 803s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '72' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 803s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 803s Warning: skipping read '74' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 803s 77 reads; of these: 803s 77 (100.00%) were unpaired; of these: 803s 69 (89.61%) aligned 0 times 803s 6 (7.79%) aligned exactly 1 time 803s 2 (2.60%) aligned >1 times 803s 10.39% overall alignment rate 803s Read 50 alignments... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s TCATTG 803s TCATTG 803s Processing line... 803s Processing line... 803s TCATTGGA 803s TCATTGGA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s GACAA 803s GACAA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CT 803s CT 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CTCAACAA 803s CTCAACAA 803s Processing line... 803s TA 803s TA 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s ACAACC 803s ACAACC 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s CCACA 803s CCACA 803s --- Summary --- 803s Read 1 reference strings 803s Checked 8 alignments, 0 edits 803s --------------- 803s PASSED 803s Flattened IUPAC characters 803s Mutating sequence Sim.pm.1 803s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutating sequence Sim.pm.2 803s Introducing 3 SNPs, 1/0 ref/read gaps, and 1 rearrangements 803s Finished SNPs 803s *** Run 65 of 100 803s /usr/bin/bowtie2 --score-min L,9.35342206761282,1.09368357991944 --gbar 12 --mp 6.09578877507804,4.31999340569574 --n-ceil 0.0835513093517448,1.02751134654436 --cp-ival 1 --local --trim3 8 --np 2 -M 2 -i L,0.265115602889483 --cp-min 8 --large-index -R 3 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 803s Finished ref gaps 803s Finished read gaps 803s Mutated reference genome to subject genome 803s SNPs introduced: 5 803s Reference gaps introduced: 1 803s Read gaps introduced: 0 803s Rearrangements introduced: 1 803s Created read sampler 803s Sampling 16 reads 803s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 803s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 803s parsing sequence Sim.pm.1... 803s parsing sequence Sim.pm.2... 803s Parsed 78 reference bases 803s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 803s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 803s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 803s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 803s 16 reads; of these: 803s 16 (100.00%) were paired; of these: 803s 16 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 16 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 16 pairs aligned 0 times concordantly or discordantly; of these: 803s 32 mates make up the pairs; of these: 803s 32 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 0.00% overall alignment rate 803s Processing line... 803s Processing line... 803s Processing line... 803s /usr/bin/bowtie2 --score-min L,9.35342206761282,1.09368357991944 --gbar 12 --mp 6.09578877507804,4.31999340569574 --n-ceil 0.0835513093517448,1.02751134654436 --cp-ival 1 --local --trim3 8 --np 2 -M 2 -i L,0.265115602889483 --cp-min 8 --large-index -R 3 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s Processing line... 803s --- Summary --- 803s Read 1 reference strings 803s Checked 0 alignments, 0 edits 803s --------------- 803s PASSED 803s ALSO checking that bowtie2 and bowtie2-align match up 803s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 803s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 803s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 803s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 803s 16 reads; of these: 803s 16 (100.00%) were paired; of these: 803s 16 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 16 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 16 pairs aligned 0 times concordantly or discordantly; of these: 803s 32 mates make up the pairs; of these: 803s 32 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 0.00% overall alignment rate 803s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 803s /usr/bin/bowtie2 --score-min L,9.35342206761282,1.09368357991944 --gbar 12 --mp 6.09578877507804,4.31999340569574 --n-ceil 0.0835513093517448,1.02751134654436 --cp-ival 1 --local --trim3 8 --np 2 -M 2 -i L,0.265115602889483 --cp-min 8 --large-index -R 3 --qseq -p 3 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 803s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 803s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 803s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 803s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 803s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 803s 16 reads; of these: 803s 16 (100.00%) were paired; of these: 803s 16 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 16 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 16 pairs aligned 0 times concordantly or discordantly; of these: 803s 32 mates make up the pairs; of these: 803s 32 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 0.00% overall alignment rate 803s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 803s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 803s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 803s /usr/bin/bowtie2 --score-min L,9.35342206761282,1.09368357991944 --gbar 12 --mp 6.09578877507804,4.31999340569574 --n-ceil 0.0835513093517448,1.02751134654436 --cp-ival 1 --local --trim3 8 --np 2 -M 2 -i L,0.265115602889483 --cp-min 8 --large-index -R 3 --qseq -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 803s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 803s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 803s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 803s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 803s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 803s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 803s 16 reads; of these: 803s 16 (100.00%) were paired; of these: 803s 16 (100.00%) aligned concordantly 0 times 803s 0 (0.00%) aligned concordantly exactly 1 time 803s 0 (0.00%) aligned concordantly >1 times 803s ---- 803s 16 pairs aligned concordantly 0 times; of these: 803s 0 (0.00%) aligned discordantly 1 time 803s ---- 803s 16 pairs aligned 0 times concordantly or discordantly; of these: 803s 32 mates make up the pairs; of these: 803s 32 (100.00%) aligned 0 times 803s 0 (0.00%) aligned exactly 1 time 803s 0 (0.00%) aligned >1 times 803s 0.00% overall alignment rate 803s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 803s Flattened IUPAC characters 803s Mutating sequence Sim.pm.2 803s Introducing 1 SNPs, 1/1 ref/read gaps, and 0 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutating sequence Sim.pm.1 803s Introducing 8 SNPs, 0/0 ref/read gaps, and 0 rearrangements 803s Finished SNPs 803s Finished ref gaps 803s Finished read gaps 803s Mutated reference genome to subject genome 803s SNPs introduced: 9 803s Reference gaps introduced: 1 803s Read gaps introduced: 1 803s Rearrangements introduced: 0 803s Created read sampler 803s Sampling 201 reads 803s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 803s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 803s parsing sequence Sim.pm.1... 803s parsing sequence Sim.pm.2... 803s Parsed 78 reference bases 803s *** Run 66 of 100 803s /usr/bin/bowtie2 -R 3 --cp-min 5 --large-index --ma 9.09018545582228 --cp-ival 2 -a --mm --score-min L,9.49557901272747,8.95131192722429 --rdg 49.6774620989264,18.2594592208294 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 803s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 803s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read '8' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 803s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 803s Warning: skipping mate #2 of read '21' because it was < 2 characters long 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 803s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 803s Read 50 alignments... 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 804s Read 100 alignments... 804s Read 150 alignments... 804s Read 200 alignments... 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 804s Warning: skipping mate #1 of read '138' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '138' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 804s Warning: skipping mate #1 of read '162' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '162' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 804s Warning: skipping mate #2 of read '165' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '165' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 804s Warning: skipping mate #2 of read '169' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '169' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 804s Warning: skipping mate #1 of read '194' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '194' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 804s Read 250 alignments... 804s Read 300 alignments... 804s 201 reads; of these: 804s 201 (100.00%) were paired; of these: 804s 201 (100.00%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 0 (0.00%) aligned concordantly >1 times 804s ---- 804s 201 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 201 pairs aligned 0 times concordantly or discordantly; of these: 804s 402 mates make up the pairs; of these: 804s 375 (93.28%) aligned 0 times 804s 14 (3.48%) aligned exactly 1 time 804s 13 (3.23%) aligned >1 times 804s 6.72% overall alignment rate 804s Read 350 alignments... 804s Read 400 alignments... 804s Read 450 alignments... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TCG 804s TCG 804s Processing line... 804s CGA 804s CGA 804s Processing line... 804s TCG 804s TCG 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CGAA 804s CGAA 804s Processing line... 804s TTCG 804s TTCG 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AAT 804s AAT 804s Processing line... 804s AAT 804s AAT 804s Processing line... 804s AAT 804s AAT 804s Processing line... 804s ATT 804s ATT 804s Processing line... 804s ATT 804s ATT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CCCGA 804s CCCGA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CGT 804s CGT 804s Processing line... 804s CGT 804s CGT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACAA 804s ACAA 804s Processing line... 804s ACAA 804s ACAA 804s Processing line... 804s ACAA 804s ACAA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s GA 804s GA 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s GA 804s GA 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s GA 804s GA 804s Processing line... 804s TC 804s TC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACA 804s ACA 804s Processing line... 804s ACA 804s ACA 804s Processing line... 804s ACA 804s ACA 804s Processing line... 804s ACA 804s ACA 804s Processing line... 804s TGT 804s TGT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TACCACAATATCACATT 804s TACCACAATATCACATT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TACCACAATATCA 804s TACCACAATATCA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACAAT 804s ACAAT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AA 804s AA 804s Processing line... 804s AA 804s AA 804s Processing line... 804s TT 804s TT 804s Processing line... 804s AA 804s AA 804s Processing line... 804s TT 804s TT 804s Processing line... 804s AA 804s AA 804s Processing line... 804s AA 804s AA 804s Processing line... 804s TT 804s TT 804s Processing line... 804s AA 804s AA 804s Processing line... 804s TT 804s TT 804s Processing line... 804s AA 804s AA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TA 804s TA 804s Processing line... 804s TA 804s TA 804s Processing line... 804s TA 804s TA 804s Processing line... 804s TA 804s TA 804s Processing line... 804s TA 804s TA 804s Processing line... 804s TA 804s TA 804s Processing line... 804s TA 804s TA 804s Processing line... 804s TA 804s TA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACCACAA 804s ACCACAA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TCGTGACAACCCGAAC 804s TCGTGACAACCCGAAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CACA 804s CACA 804s Processing line... 804s CACA 804s CACA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AATC 804s AATC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s /usr/bin/bowtie2 -R 3 --cp-min 5 --large-index --ma 9.09018545582228 --cp-ival 2 -a --mm --score-min L,9.49557901272747,8.95131192722429 --rdg 49.6774620989264,18.2594592208294 -r -p 2 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 804s Processing line... 804s Processing line... 804s CACAATATC 804s CACAATATC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TTA 804s TTA 804s Processing line... 804s TAA 804s TAA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CAATA 804s CAATA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s GA 804s GA 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s GA 804s GA 804s Processing line... 804s GA 804s GA 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s TC 804s TC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CAT 804s CAT 804s Processing line... 804s CAT 804s CAT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ATCTG 804s ATCTG 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TCGTGAC 804s TCGTGAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACT 804s ACT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CACAT 804s CACAT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACAATA 804s ACAATA 804s Processing line... 804s Processing line... 804s Processing line... 804s --- Summary --- 804s Read 1 reference strings 804s Checked 83 alignments, 0 edits 804s --------------- 804s PASSED 804s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 804s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 804s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 804s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 804s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 804s *** Run 67 of 100 804s /usr/bin/bowtie2 --score-min L,4.70037143702226,3.14881151618854 --rfg 28.6346667669465,10.8267731937932 --cp-min 6 --cp-ival 4 --large-index -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 804s Warning: skipping mate #2 of read '8' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '8' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 804s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '21' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '124; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '124; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '132; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '132; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 804s Warning: skipping mate #1 of read '138' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '138' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '176; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '176; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '188; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '188; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 804s Warning: skipping mate #1 of read '162' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '162' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 804s Warning: skipping mate #2 of read '165' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '165' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '169; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '169; setting to 0 instead 804s Warning: skipping mate #2 of read '169' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '169' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 804s Warning: skipping mate #1 of read '194' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '194' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '197; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '197; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 804s 201 reads; of these: 804s 201 (100.00%) were paired; of these: 804s 201 (100.00%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 0 (0.00%) aligned concordantly >1 times 804s ---- 804s 201 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 201 pairs aligned 0 times concordantly or discordantly; of these: 804s 402 mates make up the pairs; of these: 804s 375 (93.28%) aligned 0 times 804s 14 (3.48%) aligned exactly 1 time 804s 13 (3.23%) aligned >1 times 804s 6.72% overall alignment rate 804s Flattened IUPAC characters 804s Mutating sequence Sim.pm.2 804s Introducing 5 SNPs, 1/0 ref/read gaps, and 1 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutating sequence Sim.pm.1 804s Introducing 4 SNPs, 2/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutated reference genome to subject genome 804s SNPs introduced: 9 804s Reference gaps introduced: 3 804s Read gaps introduced: 0 804s Rearrangements introduced: 1 804s Created read sampler 804s Sampling 94 reads 804s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 804s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 804s parsing sequence Sim.pm.1... 804s parsing sequence Sim.pm.2... 804s Parsed 78 reference bases 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 804s Warning: skipping mate #1 of read '16' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '16' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 804s Warning: skipping mate #2 of read '25' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '25' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 804s Warning: skipping mate #1 of read '39' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '39' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 804s Warning: skipping mate #1 of read '57' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '57' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 804s Warning: skipping mate #2 of read '60' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '60' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 804s Read 50 alignments... 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 804s Warning: skipping mate #1 of read '65' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '65' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 804s Warning: skipping mate #2 of read '67' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '67' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 804s Warning: skipping mate #1 of read '82' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '82' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 804s Read 100 alignments... 804s 94 reads; of these: 804s 94 (100.00%) were paired; of these: 804s 93 (98.94%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 1 (1.06%) aligned concordantly >1 times 804s ---- 804s 93 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 93 pairs aligned 0 times concordantly or discordantly; of these: 804s 186 mates make up the pairs; of these: 804s 175 (94.09%) aligned 0 times 804s 5 (2.69%) aligned exactly 1 time 804s 6 (3.23%) aligned >1 times 804s 6.91% overall alignment rate 804s Read 150 alignments... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CAC 804s CAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TATCA 804s TATCA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AA 804s AA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CAAC 804s CAAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ATATCA 804s ATATCA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CAATATCAC 804s CAATATCAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AT 804s AT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TCGTGACA 804s TCGTGACA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ATT 804s ATT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CCC 804s CCC 804s Processing line... 804s CC 804s CC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AT 804s AT 804s Processing line... 804s Processing line... 804s ATCAC 804s ATCAC 804s Processing line... 804s --- Summary --- 804s Read 1 reference strings 804s Checked 13 alignments, 0 edits 804s --------------- 804s PASSED 804s Flattened IUPAC characters 804s Mutating sequence Sim.pm.1 804s Introducing 6 SNPs, 1/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutating sequence Sim.pm.2 804s Introducing 2 SNPs, 3/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutated reference genome to subject genome 804s SNPs introduced: 8 804s Reference gaps introduced: 4 804s Read gaps introduced: 0 804s Rearrangements introduced: 0 804s Created read sampler 804s Sampling 111 reads 804s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 804s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 804s parsing sequence Sim.pm.1... 804s parsing sequence Sim.pm.2... 804s Parsed 78 reference bases 804s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 804s *** Run 68 of 100 804s /usr/bin/bowtie2 --large-index --cp-min 4 -R 4 -M 3 --nofw --cp-ival 1 --n-ceil 0.039177918727567,1.03054680470213 --local --rdg 6.42934352648174 --score-min L,4.05390007215622,6.61864811861193 --mm --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 804s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 804s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 804s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 804s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 804s Warning: skipping read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 804s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 804s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 804s Warning: skipping read 'R_1_1_1_69_69_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping read 'R_1_1_1_69_69_1/1' because it was < 2 characters long 804s 111 reads; of these: 804s 111 (100.00%) were unpaired; of these: 804s 111 (100.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 0 (0.00%) aligned >1 times 804s 0.00% overall alignment rate 804s Read 50 alignments... 804s Read 100 alignments... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s --- Summary --- 804s Read 1 reference strings 804s Checked 0 alignments, 0 edits 804s --------------- 804s PASSED 804s Flattened IUPAC characters 804s Mutating sequence Sim.pm.1 804s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutating sequence Sim.pm.2 804s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutated reference genome to subject genome 804s SNPs introduced: 2 804s Reference gaps introduced: 0 804s Read gaps introduced: 0 804s Rearrangements introduced: 0 804s Created read sampler 804s Sampling 81 reads 804s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 804s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 804s parsing sequence Sim.pm.1... 804s parsing sequence Sim.pm.2... 804s Parsed 78 reference bases 804s *** Run 69 of 100 804s /usr/bin/bowtie2 --score-min L,2.68438068692217,3.49813202179094 -N 0 -L13 --mp 3.37076562853301,2.87212960893801 --cp-ival 2 --local --n-ceil 1.26675607970649,0.28478025934022 --trim3 2 -k 10 --large-index --cp-min 8 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 804s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 804s Read 50 alignments... 804s Read 100 alignments... 804s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 804s 81 reads; of these: 804s 80 (98.77%) were paired; of these: 804s 80 (100.00%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 0 (0.00%) aligned concordantly >1 times 804s ---- 804s 80 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 80 pairs aligned 0 times concordantly or discordantly; of these: 804s 160 mates make up the pairs; of these: 804s 160 (100.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 0 (0.00%) aligned >1 times 804s 1 (1.23%) were unpaired; of these: 804s 1 (100.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 0 (0.00%) aligned >1 times 804s 0.00% overall alignment rate 804s Read 150 alignments... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s --- Summary --- 804s Read 1 reference strings 804s Checked 0 alignments, 0 edits 804s --------------- 804s PASSED 804s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 804s /usr/bin/bowtie2 --score-min L,2.68438068692217,3.49813202179094 -N 0 -L13 --mp 3.37076562853301,2.87212960893801 --cp-ival 2 --local --n-ceil 1.26675607970649,0.28478025934022 --trim3 2 -k 10 --large-index --cp-min 8 --qseq -p 2 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 804s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_52_52_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 804s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 804s 81 reads; of these: 804s 80 (98.77%) were paired; of these: 804s 80 (100.00%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 0 (0.00%) aligned concordantly >1 times 804s ---- 804s 80 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 80 pairs aligned 0 times concordantly or discordantly; of these: 804s 160 mates make up the pairs; of these: 804s 160 (100.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 0 (0.00%) aligned >1 times 804s 1 (1.23%) were unpaired; of these: 804s 1 (100.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 0 (0.00%) aligned >1 times 804s 0.00% overall alignment rate 804s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 804s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 804s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 804s Flattened IUPAC characters 804s Mutating sequence Sim.pm.2 804s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutating sequence Sim.pm.1 804s Introducing 4 SNPs, 0/0 ref/read gaps, and 1 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutated reference genome to subject genome 804s SNPs introduced: 9 804s Reference gaps introduced: 0 804s Read gaps introduced: 0 804s Rearrangements introduced: 1 804s Created read sampler 804s Sampling 230 reads 804s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 804s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 804s parsing sequence Sim.pm.1... 804s parsing sequence Sim.pm.2... 804s Parsed 78 reference bases 804s *** Run 70 of 100 804s /usr/bin/bowtie2 -i S,0.376342707774197 --np 1 --score-min L,3.49636473515583,3.58071147806965 --trim3 7 --n-ceil 0.773951529891174,0.30220639667825 --cp-ival 3 --large-index --cp-min 4 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 804s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '2' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 804s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '13' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 804s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '16' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 804s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '22' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 804s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '27' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 804s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '36' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 804s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '54' because it was < 2 characters long 804s Warning: skipping mate #2 of read '54' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 804s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '60' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 804s Read 50 alignments... 804s Read 100 alignments... 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 804s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '76' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 804s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '82' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 804s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '83' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 804s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '90' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 804s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '100' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 804s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '106' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 804s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '107' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 804s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '120' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 804s Warning: skipping mate #1 of read '121' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '121' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 804s Warning: skipping mate #1 of read '136' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '136' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 804s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '138' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 804s Warning: skipping mate #1 of read '140' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '140' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 804s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '142' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 804s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '150' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 804s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '158' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 804s Warning: skipping mate #1 of read '159' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '159' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 804s Warning: skipping mate #2 of read '174' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '174' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 804s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '178' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 804s Warning: skipping mate #1 of read '182' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '182' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 804s Warning: skipping mate #1 of read '186' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '186' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 804s Warning: skipping read '188' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '188' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 804s Read 150 alignments... 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 804s Read 200 alignments... 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 804s Read 250 alignments... 804s Read 300 alignments... 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 804s Warning: skipping mate #1 of read '194' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '194' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 804s Warning: skipping mate #1 of read '195' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '195' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '197; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '201; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '201; setting to 0 instead 804s Warning: skipping mate #1 of read '201' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '201' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '204; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '209; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '209; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '210; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '210; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '211; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '212; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '213; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '213; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '214; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '214; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '215; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '215; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '216; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '216; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '217; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '217; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '218; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '218; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '219; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '219; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '220; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '220; setting to 0 instead 804s Warning: skipping mate #1 of read '220' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '220' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '221; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '221; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '222; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '222; setting to 0 instead 804s Warning: skipping mate #1 of read '222' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '222' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '223; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '223; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '224; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '224; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '225; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '225; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '226; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '226; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '227; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '228; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '228; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '229; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '229; setting to 0 instead 804s 230 reads; of these: 804s 194 (84.35%) were paired; of these: 804s 193 (99.48%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 1 (0.52%) aligned concordantly >1 times 804s ---- 804s 193 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 193 pairs aligned 0 times concordantly or discordantly; of these: 804s 386 mates make up the pairs; of these: 804s 354 (91.71%) aligned 0 times 804s 20 (5.18%) aligned exactly 1 time 804s 12 (3.11%) aligned >1 times 804s 36 (15.65%) were unpaired; of these: 804s 32 (88.89%) aligned 0 times 804s 3 (8.33%) aligned exactly 1 time 804s 1 (2.78%) aligned >1 times 804s 8.96% overall alignment rate 804s Read 350 alignments... 804s Read 400 alignments... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACCACAATATCACA 804s ACCACAATATCACA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CAT 804s CAT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ATATCA 804s ATATCA 804s Processing line... 804s Processing line... 804s Processing line... 804s CC 804s CC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACCACAATAT 804s ACCACAATAT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AACCCGA 804s AACCCGA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CAATATCA 804s CAATATCA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CA 804s CA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACAATATCAC 804s ACAATATCAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACAT 804s ACAT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ATT 804s ATT 804s Processing line... 804s Processing line... 804s CACAATATCACATT 804s CACAATATCACATT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TATCA 804s TATCA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CCC 804s CCC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACAACTCATTGG 804s ACAACTCATTGG 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TTCG 804s TTCG 804s Processing line... 804s TT 804s TT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACCCGAA 804s ACCCGAA 804s Processing line... 804s Processing line... 804s GTCGTGACAAC 804s GTCGTGACAAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TCGTGACA 804s TCGTGACA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AC 804s AC 804s Processing line... 804s Processing line... 804s AT 804s AT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TATCACA 804s TATCACA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACCACAATATCAC 804s ACCACAATATCAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AAT 804s AAT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ATTG 804s ATTG 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TTCGTCG 804s TTCGTCG 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CA 804s CA 804s Processing line... 804s Processing line... 804s GTCGTGACAACCCGAAC 804s GTCGTGACAACCCGAAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TC 804s TC 804s Processing line... 804s ACCACA 804s ACCACA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACA 804s ACA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACAA 804s ACAA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AACCCGA 804s AACCCGA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CCGAA 804s CCGAA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CA 804s CA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CCACAATATCAC 804s CCACAATATCAC 804s Processing line... 804s Processing line... 804s Processing line... 804s GTGACAACC 804s GTGACAACC 804s Processing line... 804s --- Summary --- 804s Read 1 reference strings 804s Checked 38 alignments, 0 edits 804s --------------- 804s PASSED 804s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 804s /usr/bin/bowtie2 -i S,0.376342707774197 --np 1 --score-min L,3.49636473515583,3.58071147806965 --trim3 7 --n-ceil 0.773951529891174,0.30220639667825 --cp-ival 3 --large-index --cp-min 4 -r -p 3 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 804s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '2' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 804s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '13' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 804s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '16' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 804s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '22' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 804s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '27' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 804s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '36' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 804s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '54' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '54' because it was < 2 characters long 804s Warning: skipping mate #2 of read '54' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 804s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '60' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 804s Warning: skipping mate #1 of read '76' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '76' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 804s Warning: skipping mate #1 of read '82' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '82' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 804s Warning: skipping mate #1 of read '83' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '83' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 804s Warning: skipping read '90' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '90' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 804s Warning: skipping mate #1 of read '100' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '100' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 804s Warning: skipping mate #1 of read '106' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '106' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 804s Warning: skipping mate #2 of read '107' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '107' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '116; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '116; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '117; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '117; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '118; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '118; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '119; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '119; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '120; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '120; setting to 0 instead 804s Warning: skipping mate #1 of read '120' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '120' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '121; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '121; setting to 0 instead 804s Warning: skipping mate #1 of read '121' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '121' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '122; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '122; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '123; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '123; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '125; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '125; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '126; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '126; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '127; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '127; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '128; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '128; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '129; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '129; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '130; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '130; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '131; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '131; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '133; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '133; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '134; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '134; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '135; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '135; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '136; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '136; setting to 0 instead 804s Warning: skipping mate #1 of read '136' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '136' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '137; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '137; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '138; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '138; setting to 0 instead 804s Warning: skipping mate #1 of read '138' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '138' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '139; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '139; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '140; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '140; setting to 0 instead 804s Warning: skipping mate #1 of read '140' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '140' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '141; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '141; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '142; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '142; setting to 0 instead 804s Warning: skipping mate #1 of read '142' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '142' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '143; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '143; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '144; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '144; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '145; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '145; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '146; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '146; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '147; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '147; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '148; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '148; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '149; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '149; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '150; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '150; setting to 0 instead 804s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '150' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '151; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '151; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '152; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '152; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '153; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '153; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '154; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '154; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '155; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '155; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '156; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '156; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '157; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '157; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '158; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '158; setting to 0 instead 804s Warning: skipping mate #1 of read '158' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '158' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '159; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '159; setting to 0 instead 804s Warning: skipping mate #1 of read '159' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '159' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '160; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '160; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '161; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '161; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '162; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '162; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '163; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '163; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '164; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '164; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '165; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '165; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '166; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '166; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '167; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '167; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '168; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '168; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '169; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '170; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '170; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '171; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '171; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '172; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '172; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '173; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '173; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '174; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '174; setting to 0 instead 804s Warning: skipping mate #2 of read '174' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #2 of read '174' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '175; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '175; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '176; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '177; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '177; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '178; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '178; setting to 0 instead 804s Warning: skipping mate #1 of read '178' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '178' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '179; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '179; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '180; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '180; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '181; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '181; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '182; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '182; setting to 0 instead 804s Warning: skipping mate #1 of read '182' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '182' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '183; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '183; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '184; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '184; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '185; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '185; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '186; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '186; setting to 0 instead 804s Warning: skipping mate #1 of read '186' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '186' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '187; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '187; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '188; setting to 0 instead 804s Warning: skipping read '188' because length (0) <= # seed mismatches (0) 804s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 804s Warning: skipping read '188' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '189; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '189; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '190; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '190; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '191; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '191; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '192; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '192; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '193; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '193; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '194; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '194; setting to 0 instead 804s Warning: skipping mate #1 of read '194' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '194' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '195; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '195; setting to 0 instead 804s Warning: skipping mate #1 of read '195' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '195' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '196; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '196; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '197; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '198; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '198; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '199; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '199; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '200; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '200; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '201; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '201; setting to 0 instead 804s Warning: skipping mate #1 of read '201' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '201' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '202; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '202; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '203; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '203; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '204; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '205; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '205; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '206; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '206; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '207; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '207; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '208; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '208; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '209; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '209; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '210; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '210; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '211; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '212; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '213; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '213; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '214; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '214; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '215; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '215; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '216; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '216; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '217; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '217; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '218; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '218; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '219; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '219; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '220; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '220; setting to 0 instead 804s Warning: skipping mate #1 of read '220' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '220' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '221; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '221; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '222; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '222; setting to 0 instead 804s Warning: skipping mate #1 of read '222' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '222' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '223; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '223; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '224; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '224; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '225; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '225; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '226; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '226; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '227; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '228; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '228; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '229; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '229; setting to 0 instead 804s 230 reads; of these: 804s 194 (84.35%) were paired; of these: 804s 193 (99.48%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 1 (0.52%) aligned concordantly >1 times 804s ---- 804s 193 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 193 pairs aligned 0 times concordantly or discordantly; of these: 804s 386 mates make up the pairs; of these: 804s 354 (91.71%) aligned 0 times 804s 20 (5.18%) aligned exactly 1 time 804s 12 (3.11%) aligned >1 times 804s 36 (15.65%) were unpaired; of these: 804s 32 (88.89%) aligned 0 times 804s 3 (8.33%) aligned exactly 1 time 804s 1 (2.78%) aligned >1 times 804s 8.96% overall alignment rate 804s Flattened IUPAC characters 804s Mutating sequence Sim.pm.2 804s Introducing 6 SNPs, 0/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutating sequence Sim.pm.1 804s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutated reference genome to subject genome 804s SNPs introduced: 7 804s Reference gaps introduced: 0 804s Read gaps introduced: 0 804s Rearrangements introduced: 0 804s Created read sampler 804s Sampling 80 reads 804s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 804s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 804s parsing sequence Sim.pm.1... 804s parsing sequence Sim.pm.2... 804s Parsed 78 reference bases 804s *** Run 71 of 100 804s /usr/bin/bowtie2 --score-min L,1.96408346479158,6.65023628169209 --rdg 14.9452353717503,15.9491514943903 --mm --cp-ival 1 -N 1 -L12 --trim3 8 --np 10 -i C -M 2 --cp-min 2 --large-index --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 804s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 804s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (1) 804s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 804s Read 50 alignments... 804s Read 100 alignments... 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 804s 80 reads; of these: 804s 70 (87.50%) were paired; of these: 804s 70 (100.00%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 0 (0.00%) aligned concordantly >1 times 804s ---- 804s 70 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 70 pairs aligned 0 times concordantly or discordantly; of these: 804s 140 mates make up the pairs; of these: 804s 127 (90.71%) aligned 0 times 804s 7 (5.00%) aligned exactly 1 time 804s 6 (4.29%) aligned >1 times 804s 10 (12.50%) were unpaired; of these: 804s 9 (90.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 1 (10.00%) aligned >1 times 804s 9.33% overall alignment rate 804s Read 150 alignments... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AACC 804s AACC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TC 804s TC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CCAC 804s CCAC 804s Processing line... 804s Processing line... 804s TGACAACCCG 804s TGACAACCCG 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ACAA 804s ACAA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TAATC 804s TAATC 804s Processing line... 804s Processing line... 804s ACT 804s ACT 804s Processing line... 804s Processing line... 804s GT 804s GT 804s Processing line... 804s Processing line... 804s /usr/bin/bowtie2 --score-min L,1.96408346479158,6.65023628169209 --rdg 14.9452353717503,15.9491514943903 --mm --cp-ival 1 -N 1 -L12 --trim3 8 --np 10 -i C -M 2 --cp-min 2 --large-index --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 804s Processing line... 804s Processing line... 804s CGTGACAAC 804s CGTGACAAC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AA 804s AA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CG 804s CG 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TA 804s TA 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s CACAAT 804s CACAAT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s ATC 804s ATC 804s Processing line... 804s --- Summary --- 804s Read 1 reference strings 804s Checked 14 alignments, 0 edits 804s --------------- 804s PASSED 804s ALSO checking that bowtie2 and bowtie2-align match up 804s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 804s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because length (1) <= # seed mismatches (1) 804s Warning: skipping mate #2 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_41_41_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because length (1) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 804s Warning: skipping mate #2 of read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 804s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (1) 804s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 804s 80 reads; of these: 804s 70 (87.50%) were paired; of these: 804s 70 (100.00%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 0 (0.00%) aligned concordantly >1 times 804s ---- 804s 70 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 70 pairs aligned 0 times concordantly or discordantly; of these: 804s 140 mates make up the pairs; of these: 804s 127 (90.71%) aligned 0 times 804s 7 (5.00%) aligned exactly 1 time 804s 6 (4.29%) aligned >1 times 804s 10 (12.50%) were unpaired; of these: 804s 9 (90.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 1 (10.00%) aligned >1 times 804s 9.33% overall alignment rate 804s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 804s Flattened IUPAC characters 804s Mutating sequence Sim.pm.1 804s Introducing 9 SNPs, 0/0 ref/read gaps, and 0 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutating sequence Sim.pm.2 804s Introducing 8 SNPs, 0/1 ref/read gaps, and 1 rearrangements 804s Finished SNPs 804s Finished ref gaps 804s Finished read gaps 804s Mutated reference genome to subject genome 804s SNPs introduced: 17 804s Reference gaps introduced: 0 804s Read gaps introduced: 1 804s Rearrangements introduced: 1 804s Created read sampler 804s Sampling 54 reads 804s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 804s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 804s parsing sequence Sim.pm.1... 804s parsing sequence Sim.pm.2... 804s Parsed 78 reference bases 804s *** Run 72 of 100 804s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 0.885919459770971,0.493815999000501 --nofw --mp 6.83173836800166,4.44357573832569 --trim3 8 --score-min L,8.3390838903478,2.21060252650697 --mm -a --cp-min 5 --large-index --np 3 --trim5 5 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 804s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '2' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 804s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '6' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 804s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '11' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 804s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '12' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 804s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '13' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 804s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '16' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 804s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '17' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 804s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '20' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 804s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '28' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 804s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '30' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 804s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '31' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 804s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '38' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 804s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '51' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 804s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '54' because it was < 2 characters long 804s 54 reads; of these: 804s 37 (68.52%) were paired; of these: 804s 37 (100.00%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 0 (0.00%) aligned concordantly >1 times 804s ---- 804s 37 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 37 pairs aligned 0 times concordantly or discordantly; of these: 804s 74 mates make up the pairs; of these: 804s 71 (95.95%) aligned 0 times 804s 1 (1.35%) aligned exactly 1 time 804s 2 (2.70%) aligned >1 times 804s 17 (31.48%) were unpaired; of these: 804s 17 (100.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 0 (0.00%) aligned >1 times 804s 3.30% overall alignment rate 804s Read 50 alignments... 804s Read 100 alignments... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s AT 804s AT 804s Processing line... 804s AT 804s AT 804s Processing line... 804s AT 804s AT 804s Processing line... 804s AT 804s AT 804s Processing line... 804s AT 804s AT 804s Processing line... 804s AT 804s AT 804s Processing line... 804s AT 804s AT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s GT 804s GT 804s Processing line... 804s GT 804s GT 804s Processing line... 804s GT 804s GT 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s TAATC 804s TAATC 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s Processing line... 804s --- Summary --- 804s Read 1 reference strings 804s Checked 11 alignments, 0 edits 804s --------------- 804s PASSED 804s ALSO checking that bowtie2 and bowtie2-align match up 804s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 0.885919459770971,0.493815999000501 --nofw --mp 6.83173836800166,4.44357573832569 --trim3 8 --score-min L,8.3390838903478,2.21060252650697 --mm -a --cp-min 5 --large-index --np 3 --trim5 5 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 804s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '2' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 804s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '6' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 804s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '11' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 804s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '12' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 804s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '13' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 804s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '16' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 804s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '17' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 804s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '20' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 804s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '28' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 804s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '30' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 804s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '31' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 804s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 804s Warning: skipping read '38' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 804s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '51' because it was < 2 characters long 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 804s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 804s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 804s Warning: skipping mate #1 of read '54' because it was < 2 characters long 804s 54 reads; of these: 804s 37 (68.52%) were paired; of these: 804s 37 (100.00%) aligned concordantly 0 times 804s 0 (0.00%) aligned concordantly exactly 1 time 804s 0 (0.00%) aligned concordantly >1 times 804s ---- 804s 37 pairs aligned concordantly 0 times; of these: 804s 0 (0.00%) aligned discordantly 1 time 804s ---- 804s 37 pairs aligned 0 times concordantly or discordantly; of these: 804s 74 mates make up the pairs; of these: 804s 71 (95.95%) aligned 0 times 804s 1 (1.35%) aligned exactly 1 time 804s 2 (2.70%) aligned >1 times 804s 17 (31.48%) were unpaired; of these: 804s 17 (100.00%) aligned 0 times 804s 0 (0.00%) aligned exactly 1 time 804s 0 (0.00%) aligned >1 times 804s 3.30% overall alignment rate 804s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 804s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 804s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 0.885919459770971,0.493815999000501 --nofw --mp 6.83173836800166,4.44357573832569 --trim3 8 --score-min L,8.3390838903478,2.21060252650697 --mm -a --cp-min 5 --large-index --np 3 --trim5 5 -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 805s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '2' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 805s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '6' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 805s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '11' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 805s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '12' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 805s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '13' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 805s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '16' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 805s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '17' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 805s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '20' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 805s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '28' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 805s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '30' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 805s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '31' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 805s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '38' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 805s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '51' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 805s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '54' because it was < 2 characters long 805s 54 reads; of these: 805s 37 (68.52%) were paired; of these: 805s 37 (100.00%) aligned concordantly 0 times 805s 0 (0.00%) aligned concordantly exactly 1 time 805s 0 (0.00%) aligned concordantly >1 times 805s ---- 805s 37 pairs aligned concordantly 0 times; of these: 805s 0 (0.00%) aligned discordantly 1 time 805s ---- 805s 37 pairs aligned 0 times concordantly or discordantly; of these: 805s 74 mates make up the pairs; of these: 805s 71 (95.95%) aligned 0 times 805s 1 (1.35%) aligned exactly 1 time 805s 2 (2.70%) aligned >1 times 805s 17 (31.48%) were unpaired; of these: 805s 17 (100.00%) aligned 0 times 805s 0 (0.00%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 3.30% overall alignment rate 805s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 805s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 805s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 805s /usr/bin/bowtie2 --cp-ival 3 --n-ceil 0.885919459770971,0.493815999000501 --nofw --mp 6.83173836800166,4.44357573832569 --trim3 8 --score-min L,8.3390838903478,2.21060252650697 --mm -a --cp-min 5 --large-index --np 3 --trim5 5 -q -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 805s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 805s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '2' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 805s Warning: skipping mate #1 of read '6' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '6' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 805s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '11' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 805s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '12' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 805s Warning: skipping mate #1 of read '13' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '13' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 805s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '16' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 805s Warning: skipping read '17' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '17' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 805s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '20' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 805s Warning: skipping mate #1 of read '28' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '28' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 805s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '30' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 805s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '31' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 805s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '38' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 805s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '51' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 805s Warning: skipping mate #1 of read '54' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '54' because it was < 2 characters long 805s 54 reads; of these: 805s 37 (68.52%) were paired; of these: 805s 37 (100.00%) aligned concordantly 0 times 805s 0 (0.00%) aligned concordantly exactly 1 time 805s 0 (0.00%) aligned concordantly >1 times 805s ---- 805s 37 pairs aligned concordantly 0 times; of these: 805s 0 (0.00%) aligned discordantly 1 time 805s ---- 805s 37 pairs aligned 0 times concordantly or discordantly; of these: 805s 74 mates make up the pairs; of these: 805s 71 (95.95%) aligned 0 times 805s 1 (1.35%) aligned exactly 1 time 805s 2 (2.70%) aligned >1 times 805s 17 (31.48%) were unpaired; of these: 805s 17 (100.00%) aligned 0 times 805s 0 (0.00%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 3.30% overall alignment rate 805s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 805s Flattened IUPAC characters 805s Mutating sequence Sim.pm.1 805s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutating sequence Sim.pm.2 805s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutated reference genome to subject genome 805s SNPs introduced: 7 805s Reference gaps introduced: 0 805s Read gaps introduced: 1 805s Rearrangements introduced: 0 805s Created read sampler 805s Sampling 56 reads 805s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 805s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 805s parsing sequence Sim.pm.1... 805s parsing sequence Sim.pm.2... 805s Parsed 78 reference bases 805s *** Run 73 of 100 805s /usr/bin/bowtie2 --rfg 22.4224863349979,4.68233765475391 --score-min L,9.20173286979426,8.51523766005188 --trim3 6 --nofw --n-ceil 0.502449323985815,1.41052956222324 --cp-ival 2 -D 45 -i S,1.08843860752754,0.39185417876933 --trim5 4 -k 3 --ma 14.5405480540109 --large-index --cp-min 2 --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 805s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_20_20_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_20_20_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_44_44_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_44_44_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_51_51_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 805s 56 reads; of these: 805s 56 (100.00%) were unpaired; of these: 805s 53 (94.64%) aligned 0 times 805s 3 (5.36%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 5.36% overall alignment rate 805s Read 50 alignments... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s AATAT 805s AATAT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TACCA 805s TACCA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s ACAACTCAT 805s ACAACTCAT 805s --- Summary --- 805s Read 1 reference strings 805s Checked 3 alignments, 0 edits 805s --------------- 805s PASSED 805s Flattened IUPAC characters 805s Mutating sequence Sim.pm.1 805s Introducing 1 SNPs, 1/1 ref/read gaps, and 1 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutating sequence Sim.pm.2 805s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutated reference genome to subject genome 805s SNPs introduced: 5 805s Reference gaps introduced: 1 805s Read gaps introduced: 1 805s Rearrangements introduced: 1 805s Created read sampler 805s Sampling 109 reads 805s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 805s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 805s parsing sequence Sim.pm.1... 805s parsing sequence Sim.pm.2... 805s Parsed 78 reference bases 805s *** Run 74 of 100 805s /usr/bin/bowtie2 -i C,2.47932776843331 --trim5 9 --cp-min 3 --large-index --score-min L,8.15305324178633,2.72313216722861 --rfg 7.78920362334806,4.84300926358243 --rdg 42.1942588964068,17.0471757114911 --mp 5.20437406672714,2.06268316103521 --cp-ival 1 --trim3 5 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 805s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 805s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 805s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '2' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 805s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '4' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 805s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '5' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 805s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '6' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 805s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '7' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 805s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '10' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 805s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '12' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 805s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '15' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 805s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '16' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 805s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '17' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 805s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '21' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 805s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '24' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 805s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '25' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 805s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '26' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 805s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '27' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 805s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '28' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 805s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '29' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 805s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '32' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 805s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '39' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 805s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '41' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 805s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '42' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 805s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '43' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 805s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '45' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 805s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '47' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 805s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '50' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 805s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '51' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 805s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '52' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 805s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '53' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 805s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '55' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 805s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '57' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 805s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '58' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 805s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '61' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 805s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '64' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 805s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '65' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 805s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '66' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 805s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '70' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 805s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '72' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 805s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '75' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 805s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '76' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 805s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '77' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 805s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '78' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 805s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '79' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 805s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '80' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 805s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '81' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 805s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '83' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 805s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '84' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 805s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '85' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 805s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '86' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 805s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '87' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 805s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '89' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 805s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '92' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 805s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '94' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 805s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '103' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 805s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '107' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 805s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '108' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 805s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '109' because it was < 2 characters long 805s 109 reads; of these: 805s 109 (100.00%) were unpaired; of these: 805s 103 (94.50%) aligned 0 times 805s 3 (2.75%) aligned exactly 1 time 805s 3 (2.75%) aligned >1 times 805s 5.50% overall alignment rate 805s Read 50 alignments... 805s Read 100 alignments... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s ACC 805s ACC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CACAATATCACAT 805s CACAATATCACAT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s ACAATA 805s ACAATA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CCACAATATC 805s CCACAATATC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TGTC 805s TGTC 805s Processing line... 805s AAC 805s AAC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s --- Summary --- 805s Read 1 reference strings 805s Checked 6 alignments, 0 edits 805s --------------- 805s PASSED 805s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 805s /usr/bin/bowtie2 -i C,2.47932776843331 --trim5 9 --cp-min 3 --large-index --score-min L,8.15305324178633,2.72313216722861 --rfg 7.78920362334806,4.84300926358243 --rdg 42.1942588964068,17.0471757114911 --mp 5.20437406672714,2.06268316103521 --cp-ival 1 --trim3 5 -f -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 805s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 805s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 805s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '2' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 805s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '4' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 805s Warning: skipping read '5' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '5' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 805s Warning: skipping read '6' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '6' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 805s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '7' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 805s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '10' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 805s Warning: skipping read '12' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '12' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 805s Warning: skipping read '15' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '15' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 805s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '16' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 805s Warning: skipping read '17' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '17' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 805s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '21' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 805s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '24' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 805s Warning: skipping read '25' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '25' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 805s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '26' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 805s Warning: skipping read '27' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '27' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 805s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '28' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 805s Warning: skipping read '29' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '29' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 805s Warning: skipping read '32' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '32' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 805s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '39' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 805s Warning: skipping read '41' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '41' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 805s Warning: skipping read '42' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '42' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 805s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '43' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 805s Warning: skipping read '45' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '45' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 805s Warning: skipping read '47' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '47' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 805s Warning: skipping read '50' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '50' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 805s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '51' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 805s Warning: skipping read '52' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '52' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 805s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '53' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 805s Warning: skipping read '55' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '55' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 805s Warning: skipping read '57' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '57' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 805s Warning: skipping read '58' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '58' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 805s Warning: skipping read '61' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '61' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 805s Warning: skipping read '64' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '64' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 805s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '65' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 805s Warning: skipping read '66' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '66' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 805s Warning: skipping read '70' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '70' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 805s Warning: skipping read '72' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '72' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 805s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '75' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 805s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '76' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 805s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '77' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 805s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '78' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 805s Warning: skipping read '79' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '79' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 805s Warning: skipping read '80' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '80' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 805s Warning: skipping read '81' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '81' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 805s Warning: skipping read '83' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '83' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 805s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '84' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 805s Warning: skipping read '85' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '85' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 805s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '86' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 805s Warning: skipping read '87' because length (1) <= # seed mismatches (0) 805s Warning: skipping read '87' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 805s Warning: skipping read '89' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '89' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 805s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '92' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 805s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '94' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 805s Warning: skipping read '103' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '103' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 805s Warning: skipping read '107' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '107' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 805s Warning: skipping read '108' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '108' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 805s Warning: skipping read '109' because length (0) <= # seed mismatches (0) 805s Warning: skipping read '109' because it was < 2 characters long 805s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 805s 109 reads; of these: 805s 109 (100.00%) were unpaired; of these: 805s 103 (94.50%) aligned 0 times 805s 3 (2.75%) aligned exactly 1 time 805s 3 (2.75%) aligned >1 times 805s 5.50% overall alignment rate 805s Flattened IUPAC characters 805s Mutating sequence Sim.pm.2 805s Introducing 0 SNPs, 0/1 ref/read gaps, and 1 rearrangements 805s *** Run 75 of 100 805s /usr/bin/bowtie2 --score-min L,4.21681047204365,2.69230600718689 --rdg 13.6211411220939,3.69839228380627 --mm --cp-ival 1 --local --trim3 5 --np 1 --trim5 8 -i S,0.727854076711273 --cp-min 4 --large-index --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutating sequence Sim.pm.1 805s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutated reference genome to subject genome 805s SNPs introduced: 5 805s Reference gaps introduced: 0 805s Read gaps introduced: 1 805s Rearrangements introduced: 1 805s Created read sampler 805s Sampling 85 reads 805s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 805s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 805s parsing sequence Sim.pm.1... 805s parsing sequence Sim.pm.2... 805s Parsed 78 reference bases 805s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 805s 85 reads; of these: 805s 85 (100.00%) were unpaired; of these: 805s 85 (100.00%) aligned 0 times 805s 0 (0.00%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 0.00% overall alignment rate 805s Read 50 alignments... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s --- Summary --- 805s Read 1 reference strings 805s Checked 0 alignments, 0 edits 805s --------------- 805s PASSED 805s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 805s /usr/bin/bowtie2 --score-min L,4.21681047204365,2.69230600718689 --rdg 13.6211411220939,3.69839228380627 --mm --cp-ival 1 --local --trim3 5 --np 1 --trim5 8 -i S,0.727854076711273 --cp-min 4 --large-index --qseq -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 805s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 805s 85 reads; of these: 805s 85 (100.00%) were unpaired; of these: 805s 85 (100.00%) aligned 0 times 805s 0 (0.00%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 0.00% overall alignment rate 805s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 805s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 805s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 805s /usr/bin/bowtie2 --score-min L,4.21681047204365,2.69230600718689 --rdg 13.6211411220939,3.69839228380627 --mm --cp-ival 1 --local --trim3 5 --np 1 --trim5 8 -i S,0.727854076711273 --cp-min 4 --large-index --qseq -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 805s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 805s Warning: skipping read 'R_1_1_1_2_2_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_2_2_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_4_4_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_11_11_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_11_11_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_13_13_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_13_13_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_14_14_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_14_14_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_24_24_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_24_24_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_27_27_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_37_37_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_37_37_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_38_38_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_38_38_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_39_39_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_42_42_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_45_45_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_45_45_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_46_46_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_46_46_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_79_79_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_79_79_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 805s Warning: skipping read 'R_1_1_1_84_84_1/1' because length (0) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_84_84_1/1' because it was < 2 characters long 805s 85 reads; of these: 805s 85 (100.00%) were unpaired; of these: 805s 85 (100.00%) aligned 0 times 805s 0 (0.00%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 0.00% overall alignment rate 805s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 805s Flattened IUPAC characters 805s Mutating sequence Sim.pm.2 805s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutating sequence Sim.pm.1 805s Introducing 5 SNPs, 0/0 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutated reference genome to subject genome 805s SNPs introduced: 5 805s Reference gaps introduced: 0 805s Read gaps introduced: 0 805s Rearrangements introduced: 0 805s Created read sampler 805s Sampling 131 reads 805s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 805s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 805s parsing sequence Sim.pm.1... 805s parsing sequence Sim.pm.2... 805s Parsed 78 reference bases 805s *** Run 76 of 100 805s /usr/bin/bowtie2 --ma 36.6398621869219 --cp-min 6 --cp-ival 1 --large-index --mm --score-min L,4.79469547399744,1.55362130238573 --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 805s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 805s 131 reads; of these: 805s 131 (100.00%) were unpaired; of these: 805s 112 (85.50%) aligned 0 times 805s 13 (9.92%) aligned exactly 1 time 805s 6 (4.58%) aligned >1 times 805s 14.50% overall alignment rate 805s Read 50 alignments... 805s Read 100 alignments... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s ATTGG 805s ATTGG 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CCA 805s CCA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s /usr/bin/bowtie2 --ma 36.6398621869219 --cp-min 6 --cp-ival 1 --large-index --mm --score-min L,4.79469547399744,1.55362130238573 --qseq -p 2 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TATCA 805s TATCA 805s Processing line... 805s Processing line... 805s Processing line... 805s TGACAACC 805s TGACAACC 805s Processing line... 805s TT 805s TT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TCAC 805s TCAC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TCACA 805s TCACA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s AACCCGAAC 805s AACCCGAAC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CGTCGTG 805s CGTCGTG 805s Processing line... 805s TCACA 805s TCACA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s GTCG 805s GTCG 805s Processing line... 805s Processing line... 805s ATTGGAATA 805s ATTGGAATA 805s Processing line... 805s Processing line... 805s Processing line... 805s ATATCA 805s ATATCA 805s Processing line... 805s Processing line... 805s Processing line... 805s TC 805s TC 805s Processing line... 805s Processing line... 805s Processing line... 805s ACA 805s ACA 805s Processing line... 805s Processing line... 805s Processing line... 805s TCG 805s TCG 805s Processing line... 805s Processing line... 805s Processing line... 805s TATCAC 805s TATCAC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s AACCCGAAC 805s AACCCGAAC 805s Processing line... 805s Processing line... 805s Processing line... 805s AACC 805s AACC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s --- Summary --- 805s Read 1 reference strings 805s Checked 19 alignments, 0 edits 805s --------------- 805s PASSED 805s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 805s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 805s 131 reads; of these: 805s 131 (100.00%) were unpaired; of these: 805s 112 (85.50%) aligned 0 times 805s 13 (9.92%) aligned exactly 1 time 805s 6 (4.58%) aligned >1 times 805s 14.50% overall alignment rate 805s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 805s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 805s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 805s /usr/bin/bowtie2 --ma 36.6398621869219 --cp-min 6 --cp-ival 1 --large-index --mm --score-min L,4.79469547399744,1.55362130238573 --qseq -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 805s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 805s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_33_33_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_33_33_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_56_56_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_96_96_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_104_104_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_104_104_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_110_110_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_111_111_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_112_112_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_113_113_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_114_114_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_115_115_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_116_116_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_117_117_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_118_118_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_119_119_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_120_120_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_121_121_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_122_122_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_123_123_1/1; setting to 0 instead 805s Warning: skipping read 'R_1_1_1_123_123_1/1' because length (1) <= # seed mismatches (0) 805s Warning: skipping read 'R_1_1_1_123_123_1/1' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_124_124_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_125_125_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_126_126_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_127_127_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_128_128_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_129_129_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_130_130_1/1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_131_131_1/1; setting to 0 instead 805s 131 reads; of these: 805s 131 (100.00%) were unpaired; of these: 805s 112 (85.50%) aligned 0 times 805s 13 (9.92%) aligned exactly 1 time 805s 6 (4.58%) aligned >1 times 805s 14.50% overall alignment rate 805s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 805s Flattened IUPAC characters 805s Mutating sequence Sim.pm.1 805s Introducing 3 SNPs, 1/0 ref/read gaps, and 2 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutating sequence Sim.pm.2 805s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutated reference genome to subject genome 805s SNPs introduced: 8 805s Reference gaps introduced: 1 805s Read gaps introduced: 0 805s Rearrangements introduced: 3 805s Created read sampler 805s Sampling 115 reads 805s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 805s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 805s parsing sequence Sim.pm.1... 805s parsing sequence Sim.pm.2... 805s Parsed 78 reference bases 805s *** Run 77 of 100 805s /usr/bin/bowtie2 -k 4 --trim5 0 --np 1 --rdg 26.2086381417393 --score-min L,6.58585747089139,8.4314774073081 --large-index --cp-ival 1 --n-ceil 0.727416701303059,0.785261735202394 --cp-min 6 --mp 7.35837102656324,3.9014644574488 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 805s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '53' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 805s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #2 of read '61' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 805s Read 50 alignments... 805s Read 100 alignments... 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 805s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #2 of read '103' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 805s Read 150 alignments... 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 805s Read 200 alignments... 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 805s Warning: skipping mate #2 of read '114' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #2 of read '114' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 805s 115 reads; of these: 805s 115 (100.00%) were paired; of these: 805s 115 (100.00%) aligned concordantly 0 times 805s 0 (0.00%) aligned concordantly exactly 1 time 805s 0 (0.00%) aligned concordantly >1 times 805s ---- 805s 115 pairs aligned concordantly 0 times; of these: 805s 0 (0.00%) aligned discordantly 1 time 805s ---- 805s 115 pairs aligned 0 times concordantly or discordantly; of these: 805s 230 mates make up the pairs; of these: 805s 201 (87.39%) aligned 0 times 805s 15 (6.52%) aligned exactly 1 time 805s 14 (6.09%) aligned >1 times 805s 12.61% overall alignment rate 805s Read 250 alignments... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s ACC 805s ACC 805s Processing line... 805s ACC 805s ACC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CGTGACAAC 805s CGTGACAAC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TTCGTCGTGACAACC 805s TTCGTCGTGACAACC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TACCACAAT 805s TACCACAAT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CG 805s CG 805s Processing line... 805s CG 805s CG 805s Processing line... 805s CG 805s CG 805s Processing line... 805s CG 805s CG 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TTC 805s TTC 805s Processing line... 805s GAA 805s GAA 805s Processing line... 805s GAA 805s GAA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CCCG 805s CCCG 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s GTCGTGACAA 805s GTCGTGACAA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s AT 805s AT 805s Processing line... 805s AT 805s AT 805s Processing line... 805s AT 805s AT 805s Processing line... 805s AT 805s AT 805s Processing line... 805s Processing line... 805s ACAA 805s ACAA 805s Processing line... 805s ACAA 805s ACAA 805s Processing line... 805s ACAA 805s ACAA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CCGAAC 805s CCGAAC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CCACAAT 805s CCACAAT 805s Processing line... 805s Processing line... 805s ACCCGAA 805s ACCCGAA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s ACCACAATAT 805s ACCACAATAT 805s Processing line... 805s Processing line... 805s AACCCGA 805s AACCCGA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CG 805s CG 805s Processing line... 805s CG 805s CG 805s Processing line... 805s CG 805s CG 805s Processing line... 805s CG 805s CG 805s Processing line... 805s Processing line... 805s AAC 805s AAC 805s Processing line... 805s AAC 805s AAC 805s Processing line... 805s AAC 805s AAC 805s Processing line... 805s AAC 805s AAC 805s Processing line... 805s Processing line... 805s TCTGT 805s TCTGT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CT 805s CT 805s Processing line... 805s CT 805s CT 805s Processing line... 805s CT 805s CT 805s Processing line... 805s CT 805s CT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CCACAATAT 805s CCACAATAT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TTCGTCGTGAC 805s TTCGTCGTGAC 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CA 805s CA 805s Processing line... 805s CA 805s CA 805s Processing line... 805s CA 805s CA 805s Processing line... 805s CA 805s CA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TCA 805s TCA 805s Processing line... 805s TCA 805s TCA 805s Processing line... 805s TCA 805s TCA 805s Processing line... 805s TGA 805s TGA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s ATTG 805s ATTG 805s Processing line... 805s CAAT 805s CAAT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CT 805s CT 805s Processing line... 805s CT 805s CT 805s Processing line... 805s CT 805s CT 805s Processing line... 805s CT 805s CT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CC 805s CC 805s Processing line... 805s CC 805s CC 805s Processing line... 805s CC 805s CC 805s Processing line... 805s GG 805s GG 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s CACAATA 805s CACAATA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s TT 805s TT 805s Processing line... 805s TT 805s TT 805s Processing line... 805s TT 805s TT 805s Processing line... 805s TT 805s TT 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s ACCACAATATCA 805s ACCACAATATCA 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s --- Summary --- 805s Read 1 reference strings 805s Checked 65 alignments, 0 edits 805s --------------- 805s PASSED 805s ALSO checking that bowtie2 and bowtie2-align match up 805s /usr/bin/bowtie2 -k 4 --trim5 0 --np 1 --rdg 26.2086381417393 --score-min L,6.58585747089139,8.4314774073081 --large-index --cp-ival 1 --n-ceil 0.727416701303059,0.785261735202394 --cp-min 6 --mp 7.35837102656324,3.9014644574488 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 805s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '53' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 805s Warning: skipping mate #2 of read '61' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #2 of read '61' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '90; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '90; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '102; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '102; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 805s Warning: skipping mate #2 of read '103' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #2 of read '103' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '104; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '104; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '107; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '107; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '108; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '108; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '109; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '109; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '110; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '110; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '111; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '111; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '112; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '112; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '113; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '113; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '114; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '114; setting to 0 instead 805s Warning: skipping mate #2 of read '114' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #2 of read '114' because it was < 2 characters long 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '115; setting to 0 instead 805s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '115; setting to 0 instead 805s 115 reads; of these: 805s 115 (100.00%) were paired; of these: 805s 115 (100.00%) aligned concordantly 0 times 805s 0 (0.00%) aligned concordantly exactly 1 time 805s 0 (0.00%) aligned concordantly >1 times 805s ---- 805s 115 pairs aligned concordantly 0 times; of these: 805s 0 (0.00%) aligned discordantly 1 time 805s ---- 805s 115 pairs aligned 0 times concordantly or discordantly; of these: 805s 230 mates make up the pairs; of these: 805s 201 (87.39%) aligned 0 times 805s 15 (6.52%) aligned exactly 1 time 805s 14 (6.09%) aligned >1 times 805s 12.61% overall alignment rate 805s Flattened IUPAC characters 805s Mutating sequence Sim.pm.2 805s Introducing 4 SNPs, 0/0 ref/read gaps, and 2 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutating sequence Sim.pm.1 805s Introducing 3 SNPs, 1/0 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutated reference genome to subject genome 805s SNPs introduced: 7 805s Reference gaps introduced: 1 805s Read gaps introduced: 0 805s Rearrangements introduced: 2 805s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 805s Created read sampler 805s Sampling 67 reads 805s *** Run 78 of 100 805s /usr/bin/bowtie2 --score-min L,1.34776948045958,8.84272927913442 --rfg 10.7484312614504,5.92672001420111 --rdg 28.626610010053 --mm --mp 6.38543380320159,5.52634940004894 --cp-ival 3 --local --np 2 --trim5 6 --cp-min 12 --large-index -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 805s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 805s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 805s parsing sequence Sim.pm.1... 805s parsing sequence Sim.pm.2... 805s Parsed 78 reference bases 805s Warning: skipping mate #1 of read '1' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '1' because it was < 2 characters long 805s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '4' because it was < 2 characters long 805s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '8' because it was < 2 characters long 805s Warning: skipping mate #1 of read '19' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '19' because it was < 2 characters long 805s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '28' because it was < 2 characters long 805s Warning: skipping mate #2 of read '46' because length (1) <= # seed mismatches (0) 805s Warning: skipping mate #2 of read '46' because it was < 2 characters long 805s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '52' because it was < 2 characters long 805s Warning: skipping mate #1 of read '57' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '57' because it was < 2 characters long 805s Warning: skipping mate #1 of read '61' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '61' because it was < 2 characters long 805s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 805s Warning: skipping mate #1 of read '64' because it was < 2 characters long 805s 67 reads; of these: 805s 58 (86.57%) were paired; of these: 805s 58 (100.00%) aligned concordantly 0 times 805s 0 (0.00%) aligned concordantly exactly 1 time 805s 0 (0.00%) aligned concordantly >1 times 805s ---- 805s 58 pairs aligned concordantly 0 times; of these: 805s 0 (0.00%) aligned discordantly 1 time 805s ---- 805s 58 pairs aligned 0 times concordantly or discordantly; of these: 805s 116 mates make up the pairs; of these: 805s 116 (100.00%) aligned 0 times 805s 0 (0.00%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 9 (13.43%) were unpaired; of these: 805s 9 (100.00%) aligned 0 times 805s 0 (0.00%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 0.00% overall alignment rate 805s Read 50 alignments... 805s Read 100 alignments... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s Processing line... 805s --- Summary --- 805s Read 1 reference strings 805s Checked 0 alignments, 0 edits 805s --------------- 805s PASSED 805s Flattened IUPAC characters 805s Mutating sequence Sim.pm.1 805s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutating sequence Sim.pm.2 805s Introducing 3 SNPs, 0/1 ref/read gaps, and 0 rearrangements 805s Finished SNPs 805s Finished ref gaps 805s Finished read gaps 805s Mutated reference genome to subject genome 805s SNPs introduced: 5 805s Reference gaps introduced: 0 805s Read gaps introduced: 2 805s Rearrangements introduced: 0 805s Created read sampler 805s Sampling 103 reads 806s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 806s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 806s parsing sequence Sim.pm.1... 806s parsing sequence Sim.pm.2... 806s Parsed 78 reference bases 806s *** Run 79 of 100 806s /usr/bin/bowtie2 --trim3 8 --mp 9.63362472637468,5.92100113829835 --cp-ival 3 --score-min L,9.75628732949701,1.22636314446147 --rdg 2.66507162504415 --gbar 7 --ma 38.835851840697 --cp-min 4 --large-index --trim5 6 -k 3 --norc --np 1 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 806s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 806s Warning: skipping read '4' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '4' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 806s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '5' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 806s Warning: skipping mate #1 of read '8' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '8' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 806s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '9' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 806s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '21' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 806s Warning: skipping mate #1 of read '26' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '26' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 806s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '27' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 806s Warning: skipping mate #1 of read '29' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '29' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 806s Warning: skipping mate #1 of read '31' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '31' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 806s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '32' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 806s Warning: skipping mate #1 of read '37' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '37' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 806s Warning: skipping mate #1 of read '41' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '41' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 806s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '47' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 806s Warning: skipping mate #1 of read '48' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '48' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 806s Warning: skipping mate #1 of read '49' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '49' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 806s Warning: skipping mate #1 of read '52' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '52' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 806s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '62' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 806s Warning: skipping mate #1 of read '63' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '63' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 806s Warning: skipping mate #1 of read '64' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '64' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 806s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '67' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 806s Warning: skipping read '69' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '69' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 806s Warning: skipping mate #1 of read '74' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '74' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 806s Warning: skipping mate #1 of read '76' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '76' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 806s Warning: skipping mate #1 of read '78' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '78' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 806s Warning: skipping mate #1 of read '80' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '80' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '83; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '83; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 806s Warning: skipping mate #1 of read '86' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '86' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 806s Warning: skipping mate #1 of read '95' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '95' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 806s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '96' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 806s Read 50 alignments... 806s 103 reads; of these: 806s 79 (76.70%) were paired; of these: 806s 79 (100.00%) aligned concordantly 0 times 806s 0 (0.00%) aligned concordantly exactly 1 time 806s 0 (0.00%) aligned concordantly >1 times 806s ---- 806s 79 pairs aligned concordantly 0 times; of these: 806s 0 (0.00%) aligned discordantly 1 time 806s ---- 806s 79 pairs aligned 0 times concordantly or discordantly; of these: 806s 158 mates make up the pairs; of these: 806s 149 (94.30%) aligned 0 times 806s 7 (4.43%) aligned exactly 1 time 806s 2 (1.27%) aligned >1 times 806s 24 (23.30%) were unpaired; of these: 806s 23 (95.83%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 1 (4.17%) aligned >1 times 806s 5.49% overall alignment rate 806s Read 100 alignments... 806s Read 150 alignments... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s GTCGTGACAACCCG 806s GTCGTGACAACCCG 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s CG 806s CG 806s Processing line... 806s CG 806s CG 806s Processing line... 806s CG 806s CG 806s Processing line... 806s Processing line... 806s GGAAT 806s GGAAT 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s ATCT 806s ATCT 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s TCGTCGTG 806s TCGTCGTG 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s CG 806s CG 806s Processing line... 806s CG 806s CG 806s Processing line... 806s CG 806s CG 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s GG 806s GG 806s Processing line... 806s Processing line... 806s Processing line... 806s ACAACCC 806s ACAACCC 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s ACAATATC 806s ACAATATC 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s GT 806s GT 806s Processing line... 806s GT 806s GT 806s Processing line... 806s GT 806s GT 806s --- Summary --- 806s Read 1 reference strings 806s Checked 16 alignments, 0 edits 806s --------------- 806s PASSED 806s Flattened IUPAC characters 806s Mutating sequence Sim.pm.2 806s Introducing 5 SNPs, 0/0 ref/read gaps, and 1 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutating sequence Sim.pm.1 806s *** Run 80 of 100 806s /usr/bin/bowtie2 --score-min L,8.49312548195742,2.73336041967181 --rfg 48.0117053813278,7.56212380937325 --rdg 9.90961053190608 --gbar 1 --mm --cp-min 3 --large-index --cp-ival 2 --local --trim3 5 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 806s /usr/bin/bowtie2 --score-min L,8.49312548195742,2.73336041967181 --rfg 48.0117053813278,7.56212380937325 --rdg 9.90961053190608 --gbar 1 --mm --cp-min 3 --large-index --cp-ival 2 --local --trim3 5 -q -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 806s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutated reference genome to subject genome 806s SNPs introduced: 7 806s Reference gaps introduced: 0 806s Read gaps introduced: 0 806s Rearrangements introduced: 1 806s Created read sampler 806s Sampling 50 reads 806s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 806s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 806s parsing sequence Sim.pm.1... 806s parsing sequence Sim.pm.2... 806s Parsed 78 reference bases 806s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '3' because it was < 2 characters long 806s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '7' because it was < 2 characters long 806s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '12' because it was < 2 characters long 806s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '21' because it was < 2 characters long 806s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '22' because it was < 2 characters long 806s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '24' because it was < 2 characters long 806s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '26' because it was < 2 characters long 806s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '35' because it was < 2 characters long 806s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '37' because it was < 2 characters long 806s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '44' because it was < 2 characters long 806s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '46' because it was < 2 characters long 806s 50 reads; of these: 806s 50 (100.00%) were unpaired; of these: 806s 50 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s Read 50 alignments... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s --- Summary --- 806s Read 1 reference strings 806s Checked 0 alignments, 0 edits 806s --------------- 806s PASSED 806s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 806s Warning: skipping read '3' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '3' because it was < 2 characters long 806s Warning: skipping read '7' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '7' because it was < 2 characters long 806s Warning: skipping read '12' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '12' because it was < 2 characters long 806s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '21' because it was < 2 characters long 806s Warning: skipping read '22' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '22' because it was < 2 characters long 806s Warning: skipping read '24' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '24' because it was < 2 characters long 806s Warning: skipping read '26' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '26' because it was < 2 characters long 806s Warning: skipping read '35' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '35' because it was < 2 characters long 806s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '37' because it was < 2 characters long 806s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '44' because it was < 2 characters long 806s Warning: skipping read '46' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '46' because it was < 2 characters long 806s 50 reads; of these: 806s 50 (100.00%) were unpaired; of these: 806s 50 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 806s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 806s Flattened IUPAC characters 806s Mutating sequence Sim.pm.2 806s Introducing 2 SNPs, 0/1 ref/read gaps, and 0 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutating sequence Sim.pm.1 806s Introducing 1 SNPs, 0/1 ref/read gaps, and 1 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutated reference genome to subject genome 806s SNPs introduced: 3 806s Reference gaps introduced: 0 806s Read gaps introduced: 2 806s Rearrangements introduced: 1 806s Created read sampler 806s Sampling 108 reads 806s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 806s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 806s parsing sequence Sim.pm.1... 806s parsing sequence Sim.pm.2... 806s Parsed 78 reference bases 806s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 806s *** Run 81 of 100 806s /usr/bin/bowtie2 --score-min L,7.77941869909437,5.08040601566178 --rfg 24.3257016538105 --trim3 9 --mp 4.77866675992807,2.66799644184285 --local --cp-ival 3 -M 4 --np 3 --cp-min 4 --large-index --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 806s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 806s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 806s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 806s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 806s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 806s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 806s Read 50 alignments... 806s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 806s Read 100 alignments... 806s 108 reads; of these: 806s 88 (81.48%) were paired; of these: 806s 88 (100.00%) aligned concordantly 0 times 806s 0 (0.00%) aligned concordantly exactly 1 time 806s 0 (0.00%) aligned concordantly >1 times 806s ---- 806s 88 pairs aligned concordantly 0 times; of these: 806s 0 (0.00%) aligned discordantly 1 time 806s ---- 806s 88 pairs aligned 0 times concordantly or discordantly; of these: 806s 176 mates make up the pairs; of these: 806s 176 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 20 (18.52%) were unpaired; of these: 806s 20 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s Read 150 alignments... 806s Read 200 alignments... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s /usr/bin/bowtie2 --score-min L,7.77941869909437,5.08040601566178 --rfg 24.3257016538105 --trim3 9 --mp 4.77866675992807,2.66799644184285 --local --cp-ival 3 -M 4 --np 3 --cp-min 4 --large-index --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s --- Summary --- 806s Read 1 reference strings 806s Checked 0 alignments, 0 edits 806s --------------- 806s PASSED 806s ALSO checking that bowtie2 and bowtie2-align match up 806s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 806s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_4_4_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_4_4_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_8_8_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_15_15_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_18_18_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_19_19_1/1' because it was < 2 characters long 806s Warning: skipping read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_32_32_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_39_39_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_48_48_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_52_52_1/1' because it was < 2 characters long 806s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 806s Warning: skipping read 'R_1_1_1_64_64_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_64_64_1/1' because it was < 2 characters long 806s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_78_78_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 806s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_96_96_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 806s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read 'R_1_1_1_105_105_1/1' because it was < 2 characters long 806s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 806s 108 reads; of these: 806s 88 (81.48%) were paired; of these: 806s 88 (100.00%) aligned concordantly 0 times 806s 0 (0.00%) aligned concordantly exactly 1 time 806s 0 (0.00%) aligned concordantly >1 times 806s ---- 806s 88 pairs aligned concordantly 0 times; of these: 806s 0 (0.00%) aligned discordantly 1 time 806s ---- 806s 88 pairs aligned 0 times concordantly or discordantly; of these: 806s 176 mates make up the pairs; of these: 806s 176 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 20 (18.52%) were unpaired; of these: 806s 20 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s Flattened IUPAC characters 806s Mutating sequence Sim.pm.1 806s Introducing 2 SNPs, 0/1 ref/read gaps, and 1 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutating sequence Sim.pm.2 806s Introducing 4 SNPs, 1/0 ref/read gaps, and 2 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutated reference genome to subject genome 806s SNPs introduced: 6 806s Reference gaps introduced: 1 806s Read gaps introduced: 1 806s Rearrangements introduced: 3 806s Created read sampler 806s Sampling 97 reads 806s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 806s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 806s parsing sequence Sim.pm.1... 806s parsing sequence Sim.pm.2... 806s Parsed 78 reference bases 806s *** Run 82 of 100 806s /usr/bin/bowtie2 --trim5 0 --cp-min 2 --large-index -a --score-min L,8.72277942878951,2.57803494675689 --rdg 35.3909630846381 -D 3 --cp-ival 2 --n-ceil 0.930520991140178,1.46022641152108 --local --mp 8.95053939651505,6.97341212990695 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 806s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '4' because it was < 2 characters long 806s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '20' because it was < 2 characters long 806s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '62' because it was < 2 characters long 806s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '63' because it was < 2 characters long 806s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '89' because it was < 2 characters long 806s 97 reads; of these: 806s 97 (100.00%) were unpaired; of these: 806s 97 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s Read 50 alignments... 806s Read 100 alignments... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s /usr/bin/bowtie2 --trim5 0 --cp-min 2 --large-index -a --score-min L,8.72277942878951,2.57803494675689 --rdg 35.3909630846381 -D 3 --cp-ival 2 --n-ceil 0.930520991140178,1.46022641152108 --local --mp 8.95053939651505,6.97341212990695 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s --- Summary --- 806s Read 1 reference strings 806s Checked 0 alignments, 0 edits 806s --------------- 806s PASSED 806s ALSO checking that bowtie2 and bowtie2-align match up 806s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '4' because it was < 2 characters long 806s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '20' because it was < 2 characters long 806s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '62' because it was < 2 characters long 806s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '63' because it was < 2 characters long 806s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '89' because it was < 2 characters long 806s 97 reads; of these: 806s 97 (100.00%) were unpaired; of these: 806s 97 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 806s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 806s /usr/bin/bowtie2 --trim5 0 --cp-min 2 --large-index -a --score-min L,8.72277942878951,2.57803494675689 --rdg 35.3909630846381 -D 3 --cp-ival 2 --n-ceil 0.930520991140178,1.46022641152108 --local --mp 8.95053939651505,6.97341212990695 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 806s Warning: skipping read '4' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '4' because it was < 2 characters long 806s Warning: skipping read '20' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '20' because it was < 2 characters long 806s Warning: skipping read '62' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '62' because it was < 2 characters long 806s Warning: skipping read '63' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '63' because it was < 2 characters long 806s Warning: skipping read '89' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '89' because it was < 2 characters long 806s 97 reads; of these: 806s 97 (100.00%) were unpaired; of these: 806s 97 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 806s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 806s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 806s Flattened IUPAC characters 806s Mutating sequence Sim.pm.1 806s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutating sequence Sim.pm.2 806s Introducing 3 SNPs, 0/1 ref/read gaps, and 1 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutated reference genome to subject genome 806s SNPs introduced: 3 806s Reference gaps introduced: 0 806s Read gaps introduced: 1 806s Rearrangements introduced: 1 806s Created read sampler 806s Sampling 89 reads 806s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 806s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 806s parsing sequence Sim.pm.1... 806s parsing sequence Sim.pm.2... 806s Parsed 78 reference bases 806s *** Run 83 of 100 806s /usr/bin/bowtie2 --mm --rfg 25.1792349769897 --rdg 40.3537150458739 --score-min L,5.32742438317792,7.08365419372479 -N 0 -L13 --mp 7.32522626018349,4.17029404243221 --cp-ival 2 --local --trim5 5 -k 2 --norc --large-index --cp-min 3 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 806s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '7' because it was < 2 characters long 806s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '18' because it was < 2 characters long 806s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '20' because it was < 2 characters long 806s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '22' because it was < 2 characters long 806s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '27' because it was < 2 characters long 806s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read '32' because it was < 2 characters long 806s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '45' because it was < 2 characters long 806s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '50' because it was < 2 characters long 806s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '53' because it was < 2 characters long 806s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '72' because it was < 2 characters long 806s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read '76' because it was < 2 characters long 806s Read 50 alignments... 806s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '81' because it was < 2 characters long 806s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '82' because it was < 2 characters long 806s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '87' because it was < 2 characters long 806s Read 100 alignments... 806s 89 reads; of these: 806s 80 (89.89%) were paired; of these: 806s 80 (100.00%) aligned concordantly 0 times 806s 0 (0.00%) aligned concordantly exactly 1 time 806s 0 (0.00%) aligned concordantly >1 times 806s ---- 806s 80 pairs aligned concordantly 0 times; of these: 806s 0 (0.00%) aligned discordantly 1 time 806s ---- 806s 80 pairs aligned 0 times concordantly or discordantly; of these: 806s 160 mates make up the pairs; of these: 806s 160 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 9 (10.11%) were unpaired; of these: 806s 9 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s Read 150 alignments... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s --- Summary --- 806s Read 1 reference strings 806s Checked 0 alignments, 0 edits 806s --------------- 806s PASSED 806s ALSO checking that bowtie2 and bowtie2-align match up 806s /usr/bin/bowtie2 --mm --rfg 25.1792349769897 --rdg 40.3537150458739 --score-min L,5.32742438317792,7.08365419372479 -N 0 -L13 --mp 7.32522626018349,4.17029404243221 --cp-ival 2 --local --trim5 5 -k 2 --norc --large-index --cp-min 3 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 806s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '7' because it was < 2 characters long 806s Warning: skipping read '18' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '18' because it was < 2 characters long 806s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '20' because it was < 2 characters long 806s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '22' because it was < 2 characters long 806s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '27' because it was < 2 characters long 806s Warning: skipping mate #2 of read '32' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read '32' because it was < 2 characters long 806s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '45' because it was < 2 characters long 806s Warning: skipping mate #1 of read '50' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '50' because it was < 2 characters long 806s Warning: skipping mate #1 of read '53' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '53' because it was < 2 characters long 806s Warning: skipping mate #1 of read '72' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '72' because it was < 2 characters long 806s Warning: skipping mate #2 of read '76' because length (1) <= # seed mismatches (0) 806s Warning: skipping mate #2 of read '76' because it was < 2 characters long 806s Warning: skipping mate #1 of read '81' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '81' because it was < 2 characters long 806s Warning: skipping read '82' because length (0) <= # seed mismatches (0) 806s Warning: skipping read '82' because it was < 2 characters long 806s Warning: skipping mate #1 of read '87' because length (0) <= # seed mismatches (0) 806s Warning: skipping mate #1 of read '87' because it was < 2 characters long 806s 89 reads; of these: 806s 80 (89.89%) were paired; of these: 806s 80 (100.00%) aligned concordantly 0 times 806s 0 (0.00%) aligned concordantly exactly 1 time 806s 0 (0.00%) aligned concordantly >1 times 806s ---- 806s 80 pairs aligned concordantly 0 times; of these: 806s 0 (0.00%) aligned discordantly 1 time 806s ---- 806s 80 pairs aligned 0 times concordantly or discordantly; of these: 806s 160 mates make up the pairs; of these: 806s 160 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 9 (10.11%) were unpaired; of these: 806s 9 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s Flattened IUPAC characters 806s Mutating sequence Sim.pm.2 806s Introducing 0 SNPs, 0/0 ref/read gaps, and 2 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutating sequence Sim.pm.1 806s Introducing 2 SNPs, 0/3 ref/read gaps, and 0 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutated reference genome to subject genome 806s SNPs introduced: 2 806s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 806s *** Run 84 of 100 806s /usr/bin/bowtie2 --score-min L,5.86169412929751,2.18318187937628 --rdg 33.3468264292368,14.1387096712321 -a --mm --local --cp-ival 1 -N 1 -L20 --trim3 0 --norc --trim5 9 --cp-min 4 --large-index -R 1 -r -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.raw 806s Reference gaps introduced: 0 806s Read gaps introduced: 3 806s Rearrangements introduced: 2 806s Created read sampler 806s Sampling 146 reads 806s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 806s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 806s parsing sequence Sim.pm.1... 806s parsing sequence Sim.pm.2... 806s Parsed 78 reference bases 806s Warning: skipping read '3' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '3' because it was < 2 characters long 806s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '4' because it was < 2 characters long 806s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '5' because it was < 2 characters long 806s Warning: skipping read '6' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '6' because it was < 2 characters long 806s Warning: skipping read '10' because length (1) <= # seed mismatches (1) 806s Warning: skipping read '10' because it was < 2 characters long 806s Warning: skipping read '13' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '13' because it was < 2 characters long 806s Warning: skipping read '19' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '19' because it was < 2 characters long 806s Warning: skipping read '20' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '20' because it was < 2 characters long 806s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '22' because it was < 2 characters long 806s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '23' because it was < 2 characters long 806s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '25' because it was < 2 characters long 806s Warning: skipping read '26' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '26' because it was < 2 characters long 806s Warning: skipping read '29' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '29' because it was < 2 characters long 806s Warning: skipping read '34' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '34' because it was < 2 characters long 806s Warning: skipping read '35' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '35' because it was < 2 characters long 806s Warning: skipping read '38' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '38' because it was < 2 characters long 806s Warning: skipping read '40' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '40' because it was < 2 characters long 806s Warning: skipping read '41' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '41' because it was < 2 characters long 806s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '48' because it was < 2 characters long 806s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '52' because it was < 2 characters long 806s Warning: skipping read '58' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '58' because it was < 2 characters long 806s Warning: skipping read '62' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '62' because it was < 2 characters long 806s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '67' because it was < 2 characters long 806s Warning: skipping read '80' because length (1) <= # seed mismatches (1) 806s Warning: skipping read '80' because it was < 2 characters long 806s Warning: skipping read '81' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '81' because it was < 2 characters long 806s Warning: skipping read '82' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '82' because it was < 2 characters long 806s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '83' because it was < 2 characters long 806s Warning: skipping read '89' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '89' because it was < 2 characters long 806s Warning: skipping read '91' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '91' because it was < 2 characters long 806s Warning: skipping read '92' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '92' because it was < 2 characters long 806s Warning: skipping read '93' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '93' because it was < 2 characters long 806s Warning: skipping read '94' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '94' because it was < 2 characters long 806s Warning: skipping read '98' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '98' because it was < 2 characters long 806s Warning: skipping read '99' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '99' because it was < 2 characters long 806s Warning: skipping read '101' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '101' because it was < 2 characters long 806s Warning: skipping read '103' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '103' because it was < 2 characters long 806s Warning: skipping read '105' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '105' because it was < 2 characters long 806s Warning: skipping read '108' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '108' because it was < 2 characters long 806s Warning: skipping read '109' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '109' because it was < 2 characters long 806s Warning: skipping read '112' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '112' because it was < 2 characters long 806s Warning: skipping read '115' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '115' because it was < 2 characters long 806s Warning: skipping read '119' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '119' because it was < 2 characters long 806s Warning: skipping read '121' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '121' because it was < 2 characters long 806s Warning: skipping read '126' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '126' because it was < 2 characters long 806s Warning: skipping read '129' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '129' because it was < 2 characters long 806s Warning: skipping read '132' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '132' because it was < 2 characters long 806s Warning: skipping read '133' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '133' because it was < 2 characters long 806s Warning: skipping read '136' because length (1) <= # seed mismatches (1) 806s Warning: skipping read '136' because it was < 2 characters long 806s Warning: skipping read '139' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '139' because it was < 2 characters long 806s Warning: skipping read '140' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '140' because it was < 2 characters long 806s Warning: skipping read '141' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '141' because it was < 2 characters long 806s Warning: skipping read '142' because length (1) <= # seed mismatches (1) 806s Warning: skipping read '142' because it was < 2 characters long 806s Warning: skipping read '145' because length (0) <= # seed mismatches (1) 806s Warning: skipping read '145' because it was < 2 characters long 806s 146 reads; of these: 806s 146 (100.00%) were unpaired; of these: 806s 146 (100.00%) aligned 0 times 806s 0 (0.00%) aligned exactly 1 time 806s 0 (0.00%) aligned >1 times 806s 0.00% overall alignment rate 806s Read 50 alignments... 806s Read 100 alignments... 806s Read 150 alignments... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s *** Run 85 of 100 806s /usr/bin/bowtie2 --norc --np 4 -M 6 -i S,2.18656796256931,4.86121702343386 --cp-min 7 --large-index -R 2 --score-min L,5.2342312074777,9.06082772005832 --rdg 18.6456334646227,7.14902826569388 --mm --cp-ival 1 --trim3 5 --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s --- Summary --- 806s Read 1 reference strings 806s Checked 0 alignments, 0 edits 806s --------------- 806s PASSED 806s Flattened IUPAC characters 806s Mutating sequence Sim.pm.1 806s Introducing 5 SNPs, 0/1 ref/read gaps, and 0 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutating sequence Sim.pm.2 806s Introducing 7 SNPs, 0/1 ref/read gaps, and 1 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutated reference genome to subject genome 806s SNPs introduced: 12 806s Reference gaps introduced: 0 806s Read gaps introduced: 2 806s Rearrangements introduced: 1 806s Created read sampler 806s Sampling 109 reads 806s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 806s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 806s parsing sequence Sim.pm.1... 806s parsing sequence Sim.pm.2... 806s Parsed 78 reference bases 806s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 806s 109 reads; of these: 806s 109 (100.00%) were unpaired; of these: 806s 100 (91.74%) aligned 0 times 806s 3 (2.75%) aligned exactly 1 time 806s 6 (5.50%) aligned >1 times 806s 8.26% overall alignment rate 806s Read 50 alignments... 806s Read 100 alignments... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s CAC 806s CAC 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s TA 806s TA 806s /usr/bin/bowtie2 --norc --np 4 -M 6 -i S,2.18656796256931,4.86121702343386 --cp-min 7 --large-index -R 2 --score-min L,5.2342312074777,9.06082772005832 --rdg 18.6456334646227,7.14902826569388 --mm --cp-ival 1 --trim3 5 --qseq -p 3 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s TAA 806s TAA 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s TTC 806s TTC 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s CAC 806s CAC 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s CG 806s CG 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s AA 806s AA 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s TC 806s TC 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s TTC 806s TTC 806s --- Summary --- 806s Read 1 reference strings 806s Checked 9 alignments, 0 edits 806s --------------- 806s PASSED 806s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 806s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_1_1_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_2_2_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_3_3_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_4_4_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_5_5_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_6_6_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_7_7_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_8_8_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_9_9_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_10_10_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_11_11_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_12_12_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_13_13_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_14_14_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_15_15_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_16_16_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_16_16_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_16_16_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_17_17_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_18_18_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_19_19_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_20_20_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_21_21_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_21_21_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_21_21_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_22_22_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_23_23_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_24_24_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_25_25_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_25_25_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_25_25_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_26_26_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_27_27_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_28_28_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_29_29_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_30_30_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_31_31_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_31_31_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_31_31_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_32_32_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_33_33_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_34_34_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_35_35_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_36_36_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_36_36_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_36_36_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_37_37_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_38_38_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_39_39_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_40_40_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_41_41_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_42_42_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_43_43_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_44_44_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_45_45_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_46_46_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_47_47_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_47_47_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_47_47_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_48_48_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_49_49_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_50_50_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_51_51_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_52_52_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_53_53_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_54_54_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_55_55_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_56_56_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_57_57_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_58_58_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_59_59_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_59_59_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_59_59_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_60_60_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_61_61_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_62_62_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_62_62_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_62_62_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_63_63_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_64_64_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_65_65_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_66_66_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_67_67_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_67_67_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_68_68_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_68_68_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_68_68_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_69_69_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_70_70_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_70_70_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_70_70_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_71_71_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_72_72_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_72_72_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_73_73_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_74_74_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_75_75_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_76_76_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_77_77_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_78_78_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_79_79_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_80_80_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_81_81_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_82_82_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_82_82_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_82_82_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_83_83_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_84_84_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_85_85_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_86_86_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_87_87_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_88_88_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_89_89_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_90_90_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_91_91_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_92_92_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_93_93_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_94_94_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_94_94_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_94_94_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_95_95_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_95_95_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_95_95_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_96_96_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_97_97_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (1) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_98_98_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_99_99_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_100_100_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_101_101_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_102_102_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_103_103_1/1; setting to 0 instead 806s Warning: skipping read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 806s Warning: skipping read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_104_104_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_105_105_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_106_106_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_107_107_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_108_108_1/1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read 'R_1_1_1_109_109_1/1; setting to 0 instead 806s 109 reads; of these: 806s 109 (100.00%) were unpaired; of these: 806s 100 (91.74%) aligned 0 times 806s 3 (2.75%) aligned exactly 1 time 806s 6 (5.50%) aligned >1 times 806s 8.26% overall alignment rate 806s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 806s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 806s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 806s Flattened IUPAC characters 806s Mutating sequence Sim.pm.1 806s Introducing 1 SNPs, 1/0 ref/read gaps, and 0 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s *** Run 86 of 100 806s /usr/bin/bowtie2 --large-index --cp-ival 1 --cp-min 6 -k 2 --np 1 --norc --rdg 28.1449345435572,16.958234371827 --score-min L,1.93096870143541,3.18219324317129 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 806s Mutating sequence Sim.pm.2 806s Introducing 7 SNPs, 0/0 ref/read gaps, and 1 rearrangements 806s Finished SNPs 806s Finished ref gaps 806s Finished read gaps 806s Mutated reference genome to subject genome 806s SNPs introduced: 8 806s Reference gaps introduced: 1 806s Read gaps introduced: 0 806s Rearrangements introduced: 1 806s Created read sampler 806s Sampling 95 reads 806s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 806s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 806s parsing sequence Sim.pm.1... 806s parsing sequence Sim.pm.2... 806s Parsed 78 reference bases 806s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 806s Warning: skipping read '10' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '10' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 806s Warning: skipping read '21' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '21' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 806s Warning: skipping read '22' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '22' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 806s Warning: skipping read '43' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '43' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 806s Warning: skipping read '52' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '52' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 806s Warning: skipping read '66' because length (1) <= # seed mismatches (0) 806s Warning: skipping read '66' because it was < 2 characters long 806s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 806s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 806s 95 reads; of these: 806s 95 (100.00%) were unpaired; of these: 806s 85 (89.47%) aligned 0 times 806s 3 (3.16%) aligned exactly 1 time 806s 7 (7.37%) aligned >1 times 806s 10.53% overall alignment rate 806s Read 50 alignments... 806s Read 100 alignments... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s GA 806s GA 806s Processing line... 806s GA 806s GA 806s Processing line... 806s GA 806s GA 806s Processing line... 806s GA 806s GA 806s Processing line... 806s Processing line... 806s Processing line... 806s GA 806s GA 806s Processing line... 806s GA 806s GA 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s CAACTCATTGGAAT 806s CAACTCATTGGAAT 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s AT 806s AT 806s Processing line... 806s AT 806s AT 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s ACAAC 806s ACAAC 806s Processing line... 806s ACAAC 806s ACAAC 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s CA 806s CA 806s Processing line... 806s CA 806s CA 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 806s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s ACCCGAAC 807s ACCCGAAC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CCACAATATCACAT 807s CCACAATATCACAT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TA 807s TA 807s Processing line... 807s TA 807s TA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s --- Summary --- 807s Read 1 reference strings 807s Checked 17 alignments, 0 edits 807s --------------- 807s PASSED 807s Flattened IUPAC characters 807s Mutating sequence Sim.pm.2 807s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutating sequence Sim.pm.1 807s Introducing 3 SNPs, 0/0 ref/read gaps, and 1 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutated reference genome to subject genome 807s SNPs introduced: 7 807s Reference gaps introduced: 1 807s Read gaps introduced: 0 807s Rearrangements introduced: 1 807s Created read sampler 807s Sampling 18 reads 807s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 807s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 807s parsing sequence Sim.pm.1... 807s parsing sequence Sim.pm.2... 807s Parsed 78 reference bases 807s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 807s 18 reads; of these: 807s 18 (100.00%) were paired; of these: 807s 18 (100.00%) aligned concordantly 0 times 807s 0 (0.00%) aligned concordantly exactly 1 time 807s 0 (0.00%) aligned concordantly >1 times 807s ---- 807s 18 pairs aligned concordantly 0 times; of these: 807s 1 (5.56%) aligned discordantly 1 time 807s ---- 807s 17 pairs aligned 0 times concordantly or discordantly; of these: 807s 34 mates make up the pairs; of these: 807s 32 (94.12%) aligned 0 times 807s 2 (5.88%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 11.11% overall alignment rate 807s *** Run 87 of 100 807s /usr/bin/bowtie2 --np 1 --cp-min 3 --large-index --ma 9.822747939701 -R 2 --gbar 6 --score-min L,8.84973233017477,6.93125576952321 --rfg 1.28003012705714,12.5911606551375 --rdg 13.5000808297223,15.6131876051058 --mm --cp-ival 3 --nofw --mp 9.78844248643965,3.30991156322066 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CTG 807s CTG 807s Processing line... 807s AACCCGA 807s AACCCGA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s AACCCGA 807s AACCCGA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CAAT 807s CAAT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s /usr/bin/bowtie2 --np 1 --cp-min 3 --large-index --ma 9.822747939701 -R 2 --gbar 6 --score-min L,8.84973233017477,6.93125576952321 --rfg 1.28003012705714,12.5911606551375 --rdg 13.5000808297223,15.6131876051058 --mm --cp-ival 3 --nofw --mp 9.78844248643965,3.30991156322066 -r -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 807s Processing line... 807s --- Summary --- 807s Read 1 reference strings 807s Checked 4 alignments, 0 edits 807s --------------- 807s PASSED 807s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 807s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 807s 18 reads; of these: 807s 18 (100.00%) were paired; of these: 807s 18 (100.00%) aligned concordantly 0 times 807s 0 (0.00%) aligned concordantly exactly 1 time 807s 0 (0.00%) aligned concordantly >1 times 807s ---- 807s 18 pairs aligned concordantly 0 times; of these: 807s 1 (5.56%) aligned discordantly 1 time 807s ---- 807s 17 pairs aligned 0 times concordantly or discordantly; of these: 807s 34 mates make up the pairs; of these: 807s 32 (94.12%) aligned 0 times 807s 2 (5.88%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 11.11% overall alignment rate 807s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 807s Flattened IUPAC characters 807s Mutating sequence Sim.pm.1 807s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutating sequence Sim.pm.2 807s Introducing 9 SNPs, 1/0 ref/read gaps, and 2 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutated reference genome to subject genome 807s SNPs introduced: 11 807s Reference gaps introduced: 1 807s Read gaps introduced: 0 807s Rearrangements introduced: 2 807s Created read sampler 807s Sampling 167 reads 807s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 807s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 807s parsing sequence Sim.pm.1... 807s parsing sequence Sim.pm.2... 807s Parsed 78 reference bases 807s *** Run 88 of 100 807s /usr/bin/bowtie2 --cp-ival 1 --local --trim3 9 --score-min L,7.789707892167,1.84122430603209 --rdg 15.4401742985541,16.8765881678602 --mm --cp-min 2 --large-index --norc --np 8 -k 9 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 807s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_153_153_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 807s Read 50 alignments... 807s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_164_164_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_166_166_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_166_166_1/1' because it was < 2 characters long 807s Read 100 alignments... 807s 167 reads; of these: 807s 141 (84.43%) were paired; of these: 807s 141 (100.00%) aligned concordantly 0 times 807s 0 (0.00%) aligned concordantly exactly 1 time 807s 0 (0.00%) aligned concordantly >1 times 807s ---- 807s 141 pairs aligned concordantly 0 times; of these: 807s 0 (0.00%) aligned discordantly 1 time 807s ---- 807s 141 pairs aligned 0 times concordantly or discordantly; of these: 807s 282 mates make up the pairs; of these: 807s 282 (100.00%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 26 (15.57%) were unpaired; of these: 807s 26 (100.00%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 0.00% overall alignment rate 807s Read 150 alignments... 807s Read 200 alignments... 807s Read 250 alignments... 807s Read 300 alignments... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s --- Summary --- 807s Read 1 reference strings 807s Checked 0 alignments, 0 edits 807s --------------- 807s PASSED 807s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 807s /usr/bin/bowtie2 --cp-ival 1 --local --trim3 9 --score-min L,7.789707892167,1.84122430603209 --rdg 15.4401742985541,16.8765881678602 --mm --cp-min 2 --large-index --norc --np 8 -k 9 --qseq -p 4 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 807s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_1_1_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_3_3_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_5_5_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_6_6_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_9_9_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_17_17_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_22_22_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_23_23_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_26_26_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_30_30_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_32_32_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_53_53_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_53_53_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_58_58_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because length (1) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_72_72_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_74_74_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_75_75_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_93_93_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_97_97_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_97_97_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_98_98_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_101_101_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_101_101_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_103_103_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_111_111_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_112_112_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_117_117_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because length (1) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_118_118_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_120_120_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_121_121_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_121_121_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_126_126_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_127_127_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because length (1) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_130_130_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_138_138_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_140_140_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_140_140_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_142_142_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_147_147_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_150_150_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_153_153_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_153_153_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_158_158_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_161_161_1/1' because it was < 2 characters long 807s Warning: skipping read 'R_1_1_1_164_164_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping read 'R_1_1_1_164_164_1/1' because it was < 2 characters long 807s Warning: skipping mate #1 of read 'R_1_1_1_166_166_1/1' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read 'R_1_1_1_166_166_1/1' because it was < 2 characters long 807s 167 reads; of these: 807s 141 (84.43%) were paired; of these: 807s 141 (sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 807s 100.00%) aligned concordantly 0 times 807s 0 (0.00%) aligned concordantly exactly 1 time 807s 0 (0.00%) aligned concordantly >1 times 807s ---- 807s 141 pairs aligned concordantly 0 times; of these: 807s 0 (0.00%) aligned discordantly 1 time 807s ---- 807s 141 pairs aligned 0 times concordantly or discordantly; of these: 807s 282 mates make up the pairs; of these: 807s 282 (100.00%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 26 (15.57%) were unpaired; of these: 807s 26 (100.00%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 0.00% overall alignment rate 807s Flattened IUPAC characters 807s Mutating sequence Sim.pm.1 807s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutating sequence Sim.pm.2 807s Introducing 0 SNPs, 0/0 ref/read gaps, and 0 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutated reference genome to subject genome 807s SNPs introduced: 0 807s Reference gaps introduced: 1 807s Read gaps introduced: 0 807s Rearrangements introduced: 0 807s Created read sampler 807s Sampling 61 reads 807s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 807s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 807s parsing sequence Sim.pm.1... 807s parsing sequence Sim.pm.2... 807s Parsed 78 reference bases 807s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 807s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 807s *** Run 89 of 100 807s /usr/bin/bowtie2 --cp-ival 1 --local --trim3 0 --score-min L,5.12966881786559,6.13574196050785 --rfg 46.6877811441484 --rdg 15.9391694296288,17.7106921809767 --mm --cp-min 2 --large-index -R 1 --np 11 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 807s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '23' because it was < 2 characters long 807s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '53' because it was < 2 characters long 807s 61 reads; of these: 807s 61 (100.00%) were unpaired; of these: 807s 61 (100.00%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 0.00% overall alignment rate 807s Read 50 alignments... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s /usr/bin/bowtie2 --cp-ival 1 --local --trim3 0 --score-min L,5.12966881786559,6.13574196050785 --rfg 46.6877811441484 --rdg 15.9391694296288,17.7106921809767 --mm --cp-min 2 --large-index -R 1 --np 11 -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s --- Summary --- 807s Read 1 reference strings 807s Checked 0 alignments, 0 edits 807s --------------- 807s PASSED 807s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 807s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '23' because it was < 2 characters long 807s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '53' because it was < 2 characters long 807s 61 reads; of these: 807s 61 (100.00%) were unpaired; of these: 807s 61 (100.00%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 0.00% overall alignment rate 807s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 807s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 807s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 807s /usr/bin/bowtie2 --cp-ival 1 --local --trim3 0 --score-min L,5.12966881786559,6.13574196050785 --rfg 46.6877811441484 --rdg 15.9391694296288,17.7106921809767 --mm --cp-min 2 --large-index -R 1 --np 11 -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 807s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 807s Warning: skipping read '23' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '23' because it was < 2 characters long 807s Warning: skipping read '53' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '53' because it was < 2 characters long 807s 61 reads; of these: 807s 61 (100.00%) were unpaired; of these: 807s 61 (100.00%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 0 (0.00%) aligned >1 times 807s 0.00% overall alignment rate 807s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 807s Flattened IUPAC characters 807s Mutating sequence Sim.pm.2 807s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutating sequence Sim.pm.1 807s Introducing 4 SNPs, 1/0 ref/read gaps, and 0 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutated reference genome to subject genome 807s SNPs introduced: 6 807s Reference gaps introduced: 1 807s Read gaps introduced: 0 807s Rearrangements introduced: 0 807s Created read sampler 807s Sampling 138 reads 807s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 807s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 807s parsing sequence Sim.pm.1... 807s parsing sequence Sim.pm.2... 807s Parsed 78 reference bases 807s *** Run 90 of 100 807s /usr/bin/bowtie2 --np 5 --trim5 9 -i L,0.273831033741887 --large-index --cp-min 4 --rfg 17.8625615398948 --rdg 38.5805456500251 --score-min L,2.76994456185274,8.81217771444242 -a --mm --cp-ival 1 --n-ceil 1.27441035575461,0.964131928259141 --trim3 0 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 807s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 807s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '8' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 807s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '10' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 807s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '11' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 807s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '13' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 807s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '14' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 807s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '20' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 807s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '21' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 807s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '26' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 807s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '27' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 807s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '28' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 807s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '29' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 807s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '35' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 807s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '36' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 807s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '43' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 807s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '44' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 807s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '49' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 807s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '53' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 807s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '54' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 807s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '55' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 807s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '57' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 807s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '60' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 807s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '65' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 807s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '68' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 807s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '69' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 807s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '74' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 807s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '75' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 807s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '76' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 807s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '77' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 807s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '78' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 807s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '84' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 807s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '86' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 807s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '87' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 807s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '91' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 807s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '92' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 807s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '93' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 807s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '94' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 807s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '97' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 807s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '101' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 807s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '114' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 807s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '116' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 807s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '123' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 807s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '127' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 807s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '130' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 807s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '133' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 807s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '136' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 807s 138 reads; of these: 807s 138 (100.00%) were unpaired; of these: 807s 119 (86.23%) aligned 0 times 807s 13 (9.42%) aligned exactly 1 time 807s 6 (4.35%) aligned >1 times 807s 13.77% overall alignment rate 807s Read 50 alignments... 807s Read 100 alignments... 807s Read 150 alignments... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TACCACA 807s TACCACA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s GAAT 807s GAAT 807s Processing line... 807s Processing line... 807s CA 807s CA 807s Processing line... 807s TG 807s TG 807s Processing line... 807s CA 807s CA 807s Processing line... 807s TG 807s TG 807s Processing line... 807s CA 807s CA 807s Processing line... 807s TG 807s TG 807s Processing line... 807s CA 807s CA 807s Processing line... 807s CA 807s CA 807s Processing line... 807s CA 807s CA 807s Processing line... 807s CA 807s CA 807s Processing line... 807s CA 807s CA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s GAAT 807s GAAT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s AA 807s AA 807s Processing line... 807s TT 807s TT 807s Processing line... 807s TT 807s TT 807s Processing line... 807s AA 807s AA 807s Processing line... 807s AA 807s AA 807s Processing line... 807s AA 807s AA 807s Processing line... 807s AA 807s AA 807s Processing line... 807s TT 807s TT 807s Processing line... 807s AA 807s AA 807s Processing line... 807s TT 807s TT 807s Processing line... 807s AA 807s AA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TCGTGACAAC 807s TCGTGACAAC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s AATATC 807s AATATC 807s Processing line... 807s Processing line... 807s ACA 807s ACA 807s Processing line... 807s TGT 807s TGT 807s Processing line... 807s ACA 807s ACA 807s Processing line... 807s ACA 807s ACA 807s Processing line... 807s ACA 807s ACA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CACA 807s CACA 807s Processing line... 807s CACA 807s CACA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TTCG 807s TTCG 807s Processing line... 807s CGAA 807s CGAA 807s Processing line... 807s CACAAT 807s CACAAT 807s Processing line... 807s Processing line... 807s ACT 807s ACT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s GAAT 807s GAAT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TCGTCGTGA 807s TCGTCGTGA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s ATCAC 807s ATCAC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CCG 807s CCG 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s GACAAC 807s GACAAC 807s Processing line... 807s Processing line... 807s Processing line... 807s AATATCA 807s AATATCA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s AC 807s AC 807s Processing line... 807s AC 807s AC 807s Processing line... 807s AC 807s AC 807s Processing line... 807s GT 807s GT 807s Processing line... 807s AC 807s AC 807s Processing line... 807s AC 807s AC 807s Processing line... 807s GT 807s GT 807s Processing line... 807s AC 807s AC 807s Processing line... 807s AC 807s AC 807s Processing line... 807s GT 807s GT 807s Processing line... 807s AC 807s AC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s --- Summary --- 807s Read 1 reference strings 807s Checked 55 alignments, 0 edits 807s --------------- 807s PASSED 807s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 807s /usr/bin/bowtie2 --np 5 --trim5 9 -i L,0.273831033741887 --large-index --cp-min 4 --rfg 17.8625615398948 --rdg 38.5805456500251 --score-min L,2.76994456185274,8.81217771444242 -a --mm --cp-ival 1 --n-ceil 1.27441035575461,0.964131928259141 --trim3 0 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 807s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 807s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '8' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 807s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '10' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 807s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '11' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 807s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '13' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 807s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '14' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 807s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '20' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 807s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '21' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 807s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '26' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 807s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '27' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 807s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '28' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 807s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '29' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 807s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '35' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 807s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '36' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 807s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '43' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 807s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '44' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 807s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '49' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 807s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '53' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 807s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '54' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 807s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '55' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 807s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '57' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 807s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '60' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 807s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '65' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 807s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '68' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 807s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '69' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 807s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '74' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 807s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '75' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 807s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '76' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 807s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '77' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 807s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '78' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 807s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '84' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 807s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '86' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 807s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '87' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 807s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '91' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 807s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '92' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 807s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '93' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 807s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '94' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 807s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '97' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 807s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '101' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 807s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '114' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 807s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '116' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 807s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '123' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 807s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '127' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 807s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '130' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 807s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '133' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 807s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '136' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 807s 138 reads; of these: 807s 138 (100.00%) were unpaired; of these: 807s 119 (86.23%) aligned 0 times 807s 13 (9.42%) aligned exactly 1 time 807s 6 (4.35%) aligned >1 times 807s 13.77% overall alignment rate 807s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 807s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 807s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 807s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 807s /usr/bin/bowtie2 --np 5 --trim5 9 -i L,0.273831033741887 --large-index --cp-min 4 --rfg 17.8625615398948 --rdg 38.5805456500251 --score-min L,2.76994456185274,8.81217771444242 -a --mm --cp-ival 1 --n-ceil 1.27441035575461,0.964131928259141 --trim3 0 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 807s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 807s Warning: skipping read '8' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '8' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 807s Warning: skipping read '10' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '10' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 807s Warning: skipping read '11' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '11' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 807s Warning: skipping read '13' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '13' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 807s Warning: skipping read '14' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '14' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 807s Warning: skipping read '20' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '20' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 807s Warning: skipping read '21' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '21' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 807s Warning: skipping read '26' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '26' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 807s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '27' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 807s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '28' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 807s Warning: skipping read '29' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '29' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 807s Warning: skipping read '35' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '35' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 807s Warning: skipping read '36' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '36' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 807s Warning: skipping read '43' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '43' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 807s Warning: skipping read '44' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '44' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 807s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '49' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 807s Warning: skipping read '53' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '53' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 807s Warning: skipping read '54' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '54' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 807s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '55' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 807s Warning: skipping read '57' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '57' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 807s Warning: skipping read '60' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '60' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 807s Warning: skipping read '65' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '65' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 807s Warning: skipping read '68' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '68' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 807s Warning: skipping read '69' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '69' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 807s Warning: skipping read '74' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '74' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 807s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '75' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 807s Warning: skipping read '76' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '76' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 807s Warning: skipping read '77' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '77' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 807s Warning: skipping read '78' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '78' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 807s Warning: skipping read '84' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '84' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 807s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '86' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 807s Warning: skipping read '87' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '87' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 807s Warning: skipping read '91' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '91' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 807s Warning: skipping read '92' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '92' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 807s Warning: skipping read '93' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '93' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 807s Warning: skipping read '94' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '94' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 807s Warning: skipping read '97' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '97' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 807s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '101' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '108; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '109; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '110; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '111; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '112; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '113; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '114; setting to 0 instead 807s Warning: skipping read '114' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '114' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '115; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '116; setting to 0 instead 807s Warning: skipping read '116' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '116' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '117; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '118; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '119; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '120; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '121; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '122; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '123; setting to 0 instead 807s Warning: skipping read '123' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '123' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '124; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '125; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '126; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '127; setting to 0 instead 807s Warning: skipping read '127' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '127' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '128; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '129; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '130; setting to 0 instead 807s Warning: skipping read '130' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '130' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '131; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '132; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '133; setting to 0 instead 807s Warning: skipping read '133' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '133' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '134; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '135; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '136; setting to 0 instead 807s Warning: skipping read '136' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '136' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for read '137; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '138; setting to 0 instead 807s 138 reads; of these: 807s 138 (100.00%) were unpaired; of these: 807s 119 (86.23%) aligned 0 times 807s 13 (9.42%) aligned exactly 1 time 807s 6 (4.35%) aligned >1 times 807s 13.77% overall alignment rate 807s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 807s Flattened IUPAC characters 807s Mutating sequence Sim.pm.1 807s Introducing 2 SNPs, 1/0 ref/read gaps, and 0 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutating sequence Sim.pm.2 807s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 807s Finished SNPs 807s Finished ref gaps 807s Finished read gaps 807s Mutated reference genome to subject genome 807s *** Run 91 of 100 807s /usr/bin/bowtie2 --mm --score-min L,2.53726837722017,2.72346014273079 --trim3 4 --mp 9.02916929148109,2.42963555386244 --large-index --cp-ival 1 --cp-min 2 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw 807s SNPs introduced: 6 807s Reference gaps introduced: 1 807s Read gaps introduced: 0 807s Rearrangements introduced: 0 807s Created read sampler 807s Sampling 107 reads 807s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.raw & /tmp/Sim.pm.ZMWIC0u__2.raw 807s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 807s parsing sequence Sim.pm.1... 807s parsing sequence Sim.pm.2... 807s Parsed 78 reference bases 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 807s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '4' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 807s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '11' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 807s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '12' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 807s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '37' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 807s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '44' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 807s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '58' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 807s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '62' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 807s Read 50 alignments... 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 807s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '78' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 807s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '96' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 807s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '104' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 807s Read 100 alignments... 807s 107 reads; of these: 807s 98 (91.59%) were paired; of these: 807s 98 (100.00%) aligned concordantly 0 times 807s 0 (0.00%) aligned concordantly exactly 1 time 807s 0 (0.00%) aligned concordantly >1 times 807s ---- 807s 98 pairs aligned concordantly 0 times; of these: 807s 1 (1.02%) aligned discordantly 1 time 807s ---- 807s 97 pairs aligned 0 times concordantly or discordantly; of these: 807s 194 mates make up the pairs; of these: 807s 174 (89.69%) aligned 0 times 807s 13 (6.70%) aligned exactly 1 time 807s 7 (3.61%) aligned >1 times 807s 9 (8.41%) were unpaired; of these: 807s 8 (88.89%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 1 (11.11%) aligned >1 times 807s 11.22% overall alignment rate 807s Read 150 alignments... 807s Read 200 alignments... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TCGTGACAACCCGAAC 807s TCGTGACAACCCGAAC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CCGAAC 807s CCGAAC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TACCACA 807s TACCACA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TATCACATT 807s TATCACATT 807s Processing line... 807s GTCGTGACAACC 807s GTCGTGACAACC 807s Processing line... 807s Processing line... 807s Processing line... 807s TG 807s TG 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s ATCACAT 807s ATCACAT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TCG 807s TCG 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CAATATC 807s CAATATC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s ACCACAATATCACAT 807s ACCACAATATCACAT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CC 807s CC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s GTCGTGACAACC 807s GTCGTGACAACC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s AC 807s AC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TC 807s TC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s AT 807s AT 807s Processing line... 807s Processing line... 807s ACCACAATA 807s ACCACAATA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CACAATATCACATT 807s CACAATATCACATT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s TATCAC 807s TATCAC 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CCACAATATCA 807s CCACAATATCA 807s Processing line... 807s Processing line... 807s TATCA 807s TATCA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CGT 807s CGT 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s CGTG 807s CGTG 807s Processing line... 807s CCA 807s CCA 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s Processing line... 807s --- Summary --- 807s Read 1 reference strings 807s Checked 23 alignments, 0 edits 807s --------------- 807s PASSED 807s ALSO checking that bowtie2 and bowtie2-align match up 807s /usr/bin/bowtie2 --mm --score-min L,2.53726837722017,2.72346014273079 --trim3 4 --mp 9.02916929148109,2.42963555386244 --large-index --cp-ival 1 --cp-min 2 -r -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 807s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '4' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 807s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '11' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 807s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '12' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 807s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '37' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 807s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '44' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 807s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '58' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 807s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '62' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 807s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 807s /usr/bin/bowtie2 --mm --score-min L,2.53726837722017,2.72346014273079 --trim3 4 --mp 9.02916929148109,2.42963555386244 --large-index --cp-ival 1 --cp-min 2 -r -p 4 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.raw -2 /tmp/Sim.pm.ZMWIC0u__2.raw | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 807s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 807s Warning: skipping read '78' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 807s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 807s Warning: skipping mate #1 of read '96' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 807s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 807s Warning: skipping read '104' because it was < 2 characters long 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 807s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 807s 107 reads; of these: 807s 98 (91.59%) were paired; of these: 807s 98 (100.00%) aligned concordantly 0 times 807s 0 (0.00%) aligned concordantly exactly 1 time 807s 0 (0.00%) aligned concordantly >1 times 807s ---- 807s 98 pairs aligned concordantly 0 times; of these: 807s 1 (1.02%) aligned discordantly 1 time 807s ---- 807s 97 pairs aligned 0 times concordantly or discordantly; of these: 807s 194 mates make up the pairs; of these: 807s 174 (89.69%) aligned 0 times 807s 13 (6.70%) aligned exactly 1 time 807s 7 (3.61%) aligned >1 times 807s 9 (8.41%) were unpaired; of these: 807s 8 (88.89%) aligned 0 times 807s 0 (0.00%) aligned exactly 1 time 807s 1 (11.11%) aligned >1 times 807s 11.22% overall alignment rate 807s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '0; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '0; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 808s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '4' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 808s Warning: skipping mate #1 of read '11' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '11' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 808s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '12' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '19; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '19; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '31; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '31; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '34; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '34; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 808s Warning: skipping read '37' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '37' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '38; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '38; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '42; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '42; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '43; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '43; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '44; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '44; setting to 0 instead 808s Warning: skipping mate #1 of read '44' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '44' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '49; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '49; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 808s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '58' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '62; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '62; setting to 0 instead 808s Warning: skipping mate #1 of read '62' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '62' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '64; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '64; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '66; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '66; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '68; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '68; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 808s Warning: skipping read '78' because length (1) <= # seed mismatches (0) 808s Warning: skipping read '78' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '81; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '81; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '82; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '82; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '84; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '84; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '85; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '85; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '86; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '86; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '87; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '87; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '88; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '88; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '89; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '89; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '91; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '91; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '92; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '92; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '93; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '93; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '94; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '94; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '95; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '95; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '96; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '96; setting to 0 instead 808s Warning: skipping mate #1 of read '96' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '96' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '97; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '97; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '98; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '98; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '99; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '99; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '100; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '100; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '101; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '101; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '103; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '103; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 808s Warning: skipping read '104' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '104' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '105; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '105; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '106; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '106; setting to 0 instead 808s 107 reads; of these: 808s 98 (91.59%) were paired; of these: 808s 98 (100.00%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 0 (0.00%) aligned concordantly >1 times 808s ---- 808s 98 pairs aligned concordantly 0 times; of these: 808s 1 (1.02%) aligned discordantly 1 time 808s ---- 808s 97 pairs aligned 0 times concordantly or discordantly; of these: 808s 194 mates make up the pairs; of these: 808s 174 (89.69%) aligned 0 times 808s 13 (6.70%) aligned exactly 1 time 808s 7 (3.61%) aligned >1 times 808s 9 (8.41%) were unpaired; of these: 808s 8 (88.89%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 1 (11.11%) aligned >1 times 808s 11.22% overall alignment rate 808s Flattened IUPAC characters 808s Mutating sequence Sim.pm.1 808s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutating sequence Sim.pm.2 808s Introducing 5 SNPs, 1/0 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutated reference genome to subject genome 808s SNPs introduced: 10 808s Reference gaps introduced: 2 808s Read gaps introduced: 0 808s Rearrangements introduced: 0 808s Created read sampler 808s Sampling 59 reads 808s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 808s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 808s parsing sequence Sim.pm.1... 808s parsing sequence Sim.pm.2... 808s Parsed 78 reference bases 808s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 808s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 808s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 808s *** Run 92 of 100 808s /usr/bin/bowtie2 -R 1 --large-index --cp-min 3 -k 4 --np 8 --trim3 6 -N 1 -L16 --mp 6.69117338524654,5.08896411096768 -D 30 --cp-ival 1 --local --rdg 1.49053122042453,16.2229854655237 --score-min L,8.58504670799196,9.99656750993256 --gbar 14 -f -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta 808s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '1' because it was < 2 characters long 808s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '4' because it was < 2 characters long 808s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '5' because it was < 2 characters long 808s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '8' because it was < 2 characters long 808s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '12' because it was < 2 characters long 808s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '21' because it was < 2 characters long 808s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '22' because it was < 2 characters long 808s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '23' because it was < 2 characters long 808s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '28' because it was < 2 characters long 808s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '39' because it was < 2 characters long 808s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '45' because it was < 2 characters long 808s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '48' because it was < 2 characters long 808s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '51' because it was < 2 characters long 808s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '52' because it was < 2 characters long 808s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '53' because it was < 2 characters long 808s Warning: skipping read '56' because length (1) <= # seed mismatches (1) 808s Warning: skipping read '56' because it was < 2 characters long 808s 59 reads; of these: 808s 59 (100.00%) were unpaired; of these: 808s 59 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s Read 50 alignments... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s --- Summary --- 808s Read 1 reference strings 808s Checked 0 alignments, 0 edits 808s --------------- 808s /usr/bin/bowtie2 -R 1 --large-index --cp-min 3 -k 4 --np 8 --trim3 6 -N 1 -L16 --mp 6.69117338524654,5.08896411096768 -D 30 --cp-ival 1 --local --rdg 1.49053122042453,16.2229854655237 --score-min L,8.58504670799196,9.99656750993256 --gbar 14 -f -p 2 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 808s PASSED 808s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 808s Warning: skipping read '1' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '1' because it was < 2 characters long 808s Warning: skipping read '4' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '4' because it was < 2 characters long 808s Warning: skipping read '5' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '5' because it was < 2 characters long 808s Warning: skipping read '8' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '8' because it was < 2 characters long 808s Warning: skipping read '12' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '12' because it was < 2 characters long 808s Warning: skipping read '21' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '21' because it was < 2 characters long 808s Warning: skipping read '22' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '22' because it was < 2 characters long 808s Warning: skipping read '23' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '23' because it was < 2 characters long 808s Warning: skipping read '28' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '28' because it was < 2 characters long 808s Warning: skipping read '39' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '39' because it was < 2 characters long 808s Warning: skipping read '45' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '45' because it was < 2 characters long 808s Warning: skipping read '48' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '48' because it was < 2 characters long 808s Warning: skipping read '51' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '51' because it was < 2 characters long 808s Warning: skipping read '52' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '52' because it was < 2 characters long 808s Warning: skipping read '53' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '53' because it was < 2 characters long 808s Warning: skipping read '56' because length (1) <= # seed mismatches (1) 808s Warning: skipping read '56' because it was < 2 characters long 808s 59 reads; of these: 808s 59 (100.00%) were unpaired; of these: 808s 59 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 808s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 808s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 808s Flattened IUPAC characters 808s Mutating sequence Sim.pm.2 808s Introducing 6 SNPs, 0/1 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutating sequence Sim.pm.1 808s Introducing 10 SNPs, 1/0 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutated reference genome to subject genome 808s SNPs introduced: 16 808s Reference gaps introduced: 1 808s Read gaps introduced: 1 808s Rearrangements introduced: 0 808s Created read sampler 808s Sampling 35 reads 808s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 808s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 808s parsing sequence Sim.pm.1... 808s parsing sequence Sim.pm.2... 808s Parsed 78 reference bases 808s *** Run 93 of 100 808s /usr/bin/bowtie2 --mm --gbar 2 --score-min L,9.95205932572719,6.56385647455594 --rfg 45.38236189005 --local --cp-ival 4 -D 37 --mp 6.76196685003451,3.4886773310311 -M 4 --norc --cp-min 4 --large-index --qseq -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq 808s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 808s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 808s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 808s 35 reads; of these: 808s 35 (100.00%) were unpaired; of these: 808s 35 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s --- Summary --- 808s Read 1 reference strings 808s Checked 0 alignments, 0 edits 808s --------------- 808s PASSED 808s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 808s /usr/bin/bowtie2 --mm --gbar 2 --score-min L,9.95205932572719,6.56385647455594 --rfg 45.38236189005 --local --cp-ival 4 -D 37 --mp 6.76196685003451,3.4886773310311 -M 4 --norc --cp-min 4 --large-index --qseq -p 4 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 808s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 808s Warning: skipping read 'R_1_1_1_28_28_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping read 'R_1_1_1_28_28_1/1' because it was < 2 characters long 808s Warning: skipping read 'R_1_1_1_35_35_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 808s 35 reads; of these: 808s 35 (100.00%) were unpaired; of these: 808s 35 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 808s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 808s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 808s Flattened IUPAC characters 808s Mutating sequence Sim.pm.2 808s Introducing 10 SNPs, 1/0 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutating sequence Sim.pm.1 808s Introducing 6 SNPs, 2/0 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutated reference genome to subject genome 808s SNPs introduced: 16 808s Reference gaps introduced: 3 808s Read gaps introduced: 0 808s Rearrangements introduced: 0 808s Created read sampler 808s Sampling 151 reads 808s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 808s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 808s parsing sequence Sim.pm.1... 808s parsing sequence Sim.pm.2... 808s Parsed 78 reference bases 808s *** Run 94 of 100 808s /usr/bin/bowtie2 --cp-min 2 --large-index --trim5 7 --np 9 --nofw -N 1 -L12 --local --cp-ival 5 --mm --score-min L,4.48830744275178,5.38411454933218 --rdg 3.7592829254172,3.74106930894353 --rfg 31.8204797831088,9.41582039480318 -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 808s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '4' because it was < 2 characters long 808s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '10' because it was < 2 characters long 808s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '12' because it was < 2 characters long 808s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '17' because it was < 2 characters long 808s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '23' because it was < 2 characters long 808s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '25' because it was < 2 characters long 808s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '45' because it was < 2 characters long 808s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '47' because it was < 2 characters long 808s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '53' because it was < 2 characters long 808s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '58' because it was < 2 characters long 808s Read 50 alignments... 808s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '67' because it was < 2 characters long 808s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '71' because it was < 2 characters long 808s Read 100 alignments... 808s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '83' because it was < 2 characters long 808s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '91' because it was < 2 characters long 808s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '98' because it was < 2 characters long 808s Warning: skipping read '105' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '105' because it was < 2 characters long 808s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '114' because it was < 2 characters long 808s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '125' because it was < 2 characters long 808s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '128' because it was < 2 characters long 808s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '130' because it was < 2 characters long 808s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '139' because it was < 2 characters long 808s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '150' because it was < 2 characters long 808s Read 150 alignments... 808s 151 reads; of these: 808s 130 (86.09%) were paired; of these: 808s 130 (100.00%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 0 (0.00%) aligned concordantly >1 times 808s ---- 808s 130 pairs aligned concordantly 0 times; of these: 808s 0 (0.00%) aligned discordantly 1 time 808s ---- 808s 130 pairs aligned 0 times concordantly or discordantly; of these: 808s 260 mates make up the pairs; of these: 808s 260 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 21 (13.91%) were unpaired; of these: 808s 21 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s Read 200 alignments... 808s Read 250 alignments... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s /usr/bin/bowtie2 --cp-min 2 --large-index --trim5 7 --np 9 --nofw -N 1 -L12 --local --cp-ival 5 --mm --score-min L,4.48830744275178,5.38411454933218 --rdg 3.7592829254172,3.74106930894353 --rfg 31.8204797831088,9.41582039480318 -q -p 4 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s --- Summary --- 808s Read 1 reference strings 808s Checked 0 alignments, 0 edits 808s --------------- 808s PASSED 808s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 808s Warning: skipping mate #1 of read '4' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '4' because it was < 2 characters long 808s Warning: skipping mate #1 of read '10' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '10' because it was < 2 characters long 808s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '12' because it was < 2 characters long 808s Warning: skipping read '17' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '17' because it was < 2 characters long 808s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '23' because it was < 2 characters long 808s Warning: skipping read '25' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '25' because it was < 2 characters long 808s Warning: skipping mate #1 of read '45' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '45' because it was < 2 characters long 808s Warning: skipping mate #1 of read '47' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '47' because it was < 2 characters long 808s Warning: skipping mate #1 of read '53' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '53' because it was < 2 characters long 808s Warning: skipping mate #1 of read '58' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '58' because it was < 2 characters long 808s Warning: skipping read '67' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '67' because it was < 2 characters long 808s Warning: skipping mate #1 of read '71' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '71' because it was < 2 characters long 808s Warning: skipping read '83' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '83' because it was < 2 characters long 808s Warning: skipping mate #1 of read '91' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '91' because it was < 2 characters long 808s Warning: skipping mate #1 of read '98' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '98' because it was < 2 characters long 808s Warning: skipping read '105' because length (0) <= # seed mismatches (1) 808s Warning: skipping read '105' because it was < 2 characters long 808s Warning: skipping mate #1 of read '114' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '114' because it was < 2 characters long 808s Warning: skipping mate #1 of read '125' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '125' because it was < 2 characters long 808s Warning: skipping mate #1 of read '128' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '128' because it was < 2 characters long 808s Warning: skipping mate #1 of read '130' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '130' because it was < 2 characters long 808s Warning: skipping mate #1 of read '139' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '139' because it was < 2 characters long 808s Warning: skipping mate #1 of read '150' because length (0) <= # seed mismatches (1) 808s Warning: skipping mate #1 of read '150' because it was < 2 characters long 808s 151 reads; of these: 808s 130 (86.09%) were paired; of these: 808s 130 (100.00%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 0 (0.00%) aligned concordantly >1 times 808s ---- 808s 130 pairs aligned concordantly 0 times; of these: 808s 0 (0.00%) aligned discordantly 1 time 808s ---- 808s 130 pairs aligned 0 times concordantly or discordantly; of these: 808s 260 mates make up the pairs; of these: 808s 260 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 21 (13.91%) were unpaired; of these: 808s 21 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 808s Flattened IUPAC characters 808s Mutating sequence Sim.pm.1 808s Introducing 5 SNPs, 1/2 ref/read gaps, and 1 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutating sequence Sim.pm.2 808s Introducing 9 SNPs, 0/2 ref/read gaps, and 1 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutated reference genome to subject genome 808s SNPs introduced: 14 808s Reference gaps introduced: 1 808s Read gaps introduced: 4 808s Rearrangements introduced: 2 808s Created read sampler 808s Sampling 90 reads 808s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 808s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 808s parsing sequence Sim.pm.1... 808s parsing sequence Sim.pm.2... 808s Parsed 78 reference bases 808s *** Run 95 of 100 808s /usr/bin/bowtie2 --cp-min 3 --large-index --trim5 5 --np 2 --trim3 5 --cp-ival 3 --local --mp 9.63626380222031,3.40262578438185 --mm --score-min L,7.25723012577023,5.58823546208442 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 808s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_7_7_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_10_10_1/1' because it was < 2 characters long 808s Warning: skipping read 'R_1_1_1_12_12_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping read 'R_1_1_1_12_12_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_34_34_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_35_35_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_40_40_1/1' because it was < 2 characters long 808s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_51_51_1/1' because it was < 2 characters long 808s Warning: skipping read 'R_1_1_1_54_54_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping read 'R_1_1_1_54_54_1/1' because it was < 2 characters long 808s Warning: skipping read 'R_1_1_1_55_55_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping read 'R_1_1_1_55_55_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_57_57_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 808s Warning: skipping mate #2 of read 'R_1_1_1_57_57_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_61_61_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_63_63_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_65_65_1/1' because it was < 2 characters long 808s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_67_67_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 808s Warning: skipping mate #2 of read 'R_1_1_1_73_73_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_76_76_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_80_80_1/1' because it was < 2 characters long 808s Warning: skipping read 'R_1_1_1_83_83_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping read 'R_1_1_1_83_83_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_87_87_1/1' because it was < 2 characters long 808s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_89_89_1/1' because it was < 2 characters long 808s Read 50 alignments... 808s Read 100 alignments... 808s 90 reads; of these: 808s 72 (80.00%) were paired; of these: 808s 72 (100.00%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 0 (0.00%) aligned concordantly >1 times 808s ---- 808s 72 pairs aligned concordantly 0 times; of these: 808s 0 (0.00%) aligned discordantly 1 time 808s ---- 808s 72 pairs aligned 0 times concordantly or discordantly; of these: 808s 144 mates make up the pairs; of these: 808s 144 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 18 (20.00%) were unpaired; of these: 808s 18 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s Read 150 alignments... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s --- Summary --- 808s Read 1 reference strings 808s Checked 0 alignments, 0 edits 808s --------------- 808s PASSED 808s Flattened IUPAC characters 808s Mutating sequence Sim.pm.1 808s Introducing 7 SNPs, 0/0 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutating sequence Sim.pm.2 808s Introducing 3 SNPs, 0/0 ref/read gaps, and 2 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutated reference genome to subject genome 808s SNPs introduced: 10 808s Reference gaps introduced: 0 808s Read gaps introduced: 0 808s Rearrangements introduced: 2 808s Created read sampler 808s Sampling 31 reads 808s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 808s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 808s parsing sequence Sim.pm.1... 808s parsing sequence Sim.pm.2... 808s Parsed 78 reference bases 808s *** Run 96 of 100 808s /usr/bin/bowtie2 --ma 16.986152821138 --large-index --cp-min 4 -N 0 -L15 --mp 9.01245153046138,7.53699599515864 --cp-ival 1 --trim3 9 --score-min L,4.60220860978017,8.39061870807903 --mm -q -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq 808s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 808s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '2' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 808s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '9' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 808s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '19' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 808s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '20' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 808s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '22' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 808s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '23' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 808s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '27' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 808s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '30' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 808s 31 reads; of these: 808s 21 (67.74%) were paired; of these: 808s 21 (100.00%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 0 (0.00%) aligned concordantly >1 times 808s ---- 808s 21 pairs aligned concordantly 0 times; of these: 808s 0 (0.00%) aligned discordantly 1 time 808s ---- 808s 21 pairs aligned 0 times concordantly or discordantly; of these: 808s 42 mates make up the pairs; of these: 808s 42 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 10 (32.26%) were unpaired; of these: 808s 10 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s Read 50 alignments... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s --- Summary --- 808s Read 1 reference strings 808s Checked 0 alignments, 0 edits 808s --------------- 808s PASSED 808s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 808s /usr/bin/bowtie2 --ma 16.986152821138 --large-index --cp-min 4 -N 0 -L15 --mp 9.01245153046138,7.53699599515864 --cp-ival 1 --trim3 9 --score-min L,4.60220860978017,8.39061870807903 --mm -q -p 3 -x /tmp/Sim.pm.ZMWIC0u_ --reorder -1 /tmp/Sim.pm.ZMWIC0u__1.fastq -2 /tmp/Sim.pm.ZMWIC0u__2.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 808s Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 808s Warning: skipping read '2' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '2' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '3; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '3; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 808s Warning: skipping mate #1 of read '9' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '9' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 808s Warning: skipping read '19' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '19' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 808s Warning: skipping mate #1 of read '20' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '20' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 808s Warning: skipping mate #1 of read '22' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '22' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 808s Warning: skipping mate #1 of read '23' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '23' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '25; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '25; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '26; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '26; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 808s Warning: skipping read '27' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '27' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '30; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '30; setting to 0 instead 808s Warning: skipping mate #1 of read '30' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '30' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 808s 31 reads; of these: 808s 21 (67.74%) were paired; of these: 808s 21 (100.00%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 0 (0.00%) aligned concordantly >1 times 808s ---- 808s 21 pairs aligned concordantly 0 times; of these: 808s 0 (0.00%) aligned discordantly 1 time 808s ---- 808s 21 pairs aligned 0 times concordantly or discordantly; of these: 808s 42 mates make up the pairs; of these: 808s 42 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 10 (32.26%) were unpaired; of these: 808s 10 (100.00%) aligned 0 times 808s 0 (0.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 0.00% overall alignment rate 808s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 808s Flattened IUPAC characters 808s Mutating sequence Sim.pm.2 808s Introducing 1 SNPs, 0/0 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutating sequence Sim.pm.1 808s Introducing 4 SNPs, 2/0 ref/read gaps, and 2 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutated reference genome to subject genome 808s SNPs introduced: 5 808s Reference gaps introduced: 2 808s Read gaps introduced: 0 808s Rearrangements introduced: 2 808s Created read sampler 808s Sampling 144 reads 808s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.qseq & /tmp/Sim.pm.ZMWIC0u__2.qseq 808s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 808s parsing sequence Sim.pm.1... 808s parsing sequence Sim.pm.2... 808s Parsed 78 reference bases 808s *** Run 97 of 100 808s /usr/bin/bowtie2 --cp-min 2 --large-index --np 5 --cp-ival 2 --n-ceil 0.85757171124853,1.23819307831415 --mp 5.60490769679526,2.66494071414692 --gbar 2 --score-min L,2.10934854126285,1.2027180419448 --rdg 18.9355443718477 --rfg 36.8864228605972,15.2464302354243 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 808s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 808s Read 50 alignments... 808s Read 100 alignments... 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_77_77_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 808s Read 150 alignments... 808s 144 reads; of these: 808s 144 (100.00%) were paired; of these: 808s 143 (99.31%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 1 (0.69%) aligned concordantly >1 times 808s ---- 808s 143 pairs aligned concordantly 0 times; of these: 808s 2 (1.40%) aligned discordantly 1 time 808s ---- 808s 141 pairs aligned 0 times concordantly or discordantly; of these: 808s 282 mates make up the pairs; of these: 808s 253 (89.72%) aligned 0 times 808s 16 (5.67%) aligned exactly 1 time 808s 13 (4.61%) aligned >1 times 808s 12.15% overall alignment rate 808s Read 200 alignments... 808s Read 250 alignments... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s TA 808s TA 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s CCAC 808s CCAC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s GAA 808s GAA 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s CGTGACAACCCGA 808s CGTGACAACCCGA 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s TCACAT 808s TCACAT 808s Processing line... 808s Processing line... 808s CCACAATATC 808s CCACAATATC 808s Processing line... 808s Processing line... 808s TTCGTCGTGACAACC 808s TTCGTCGTGACAACC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s AA 808s AA 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s TAAT 808s TAAT 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s CCA 808s CCA 808s Processing line... 808s CAATATC 808s CAATATC 808s Processing line... 808s CGTGACA 808s CGTGACA 808s Processing line... 808s Processing line... 808s GTC 808s GTC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s ACCACAATATCACA 808s ACCACAATATCACA 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s AC 808s AC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s TGAC 808s TGAC 808s Processing line... 808s GTCGTGACAACCCGAAC 808s GTCGTGACAACCCGAAC 808s Processing line... 808s Processing line... 808s Processing line... 808s AT 808s AT 808s Processing line... 808s Processing line... 808s TG 808s TG 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s TCACATT 808s TCACATT 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s ACCACAATATCACA 808s ACCACAATATCACA 808s Processing line... 808s Processing line... 808s CGTGACAACCC 808s CGTGACAACCC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s AACT 808s AACT 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s AATATCACAT 808s AATATCACAT 808s Processing line... 808s Processing line... 808s CAT 808s CAT 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s CACAAT 808s CACAAT 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s ACAACCCGAA 808s ACAACCCGAA 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s ACAT 808s ACAT 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s CAA 808s CAA 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s CACA 808s CACA 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s AAT 808s AAT 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s TC 808s TC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s AC 808s AC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s GTCGTGACAA 808s GTCGTGACAA 808s Processing line... 808s ATCT 808s ATCT 808s --- Summary --- 808s Read 1 reference strings 808s Checked 35 alignments, 0 edits 808s --------------- 808s PASSED 808s ALSO checking that bowtie2 and bowtie2-align match up 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 808s /usr/bin/bowtie2 --cp-min 2 --large-index --np 5 --cp-ival 2 --n-ceil 0.85757171124853,1.23819307831415 --mp 5.60490769679526,2.66494071414692 --gbar 2 --score-min L,2.10934854126285,1.2027180419448 --rdg 18.9355443718477 --rfg 36.8864228605972,15.2464302354243 --qseq -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.qseq -2 /tmp/Sim.pm.ZMWIC0u__2.qseq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_1_1_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_2_2_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_3_3_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_4_4_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_5_5_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_6_6_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_7_7_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_8_8_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_9_9_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_10_10_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_11_11_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_12_12_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_13_13_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_14_14_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_15_15_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_16_16_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_17_17_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_18_18_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_19_19_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_20_20_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_21_21_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_22_22_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_23_23_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_24_24_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_25_25_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_26_26_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_27_27_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_27_27_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_28_28_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_29_29_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_30_30_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_31_31_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_32_32_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_33_33_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_34_34_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_35_35_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_36_36_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_37_37_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_38_38_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_39_39_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_40_40_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_41_41_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_42_42_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_42_42_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_42_42_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_43_43_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_44_44_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_45_45_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_46_46_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_47_47_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_48_48_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_49_49_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_49_49_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_50_50_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_50_50_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_51_51_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_52_52_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_53_53_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_54_54_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_55_55_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_56_56_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_57_57_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_58_58_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_59_59_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_60_60_1/1; setting to 0 instead 808s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read 'R_1_1_1_60_60_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_61_61_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_62_62_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_63_63_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_64_64_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_65_65_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_66_66_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_67_67_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_68_68_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_69_69_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_70_70_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_71_71_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_72_72_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_73_73_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_74_74_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_75_75_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_76_76_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_77_77_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_77_77_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_77_77_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_78_78_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_79_79_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_80_80_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_81_81_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_82_82_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_83_83_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_84_84_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_85_85_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_86_86_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_87_87_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_88_88_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_89_89_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_90_90_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_91_91_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_92_92_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_93_93_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_94_94_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_95_95_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_96_96_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_97_97_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_98_98_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_99_99_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_100_100_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_101_101_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_102_102_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_103_103_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_104_104_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_105_105_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_106_106_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_107_107_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_108_108_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_109_109_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_110_110_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_111_111_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_112_112_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_113_113_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_114_114_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_115_115_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_116_116_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_117_117_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_118_118_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_119_119_1/1; setting to 0 instead 808s Warning: skipping mate #2 of read 'R_1_1_1_119_119_1/1' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read 'R_1_1_1_119_119_1/1' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_120_120_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_121_121_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_122_122_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_123_123_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_124_124_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_125_125_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_126_126_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_127_127_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_128_128_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_129_129_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_130_130_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_131_131_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_132_132_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_133_133_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_134_134_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_135_135_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_136_136_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_137_137_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_138_138_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_139_139_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_140_140_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_141_141_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_142_142_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_143_143_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read 'R_1_1_1_144_144_1/1; setting to 0 instead 808s 144 reads; of these: 808s 144 (100.00%) were paired; of these: 808s 143 (99.31%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 1 (0.69%) aligned concordantly >1 times 808s ---- 808s 143 pairs aligned concordantly 0 times; of these: 808s 2 (1.40%) aligned discordantly 1 time 808s ---- 808s 141 pairs aligned 0 times concordantly or discordantly; of these: 808s 282 mates make up the pairs; of these: 808s 253 (89.72%) aligned 0 times 808s 16 (5.67%) aligned exactly 1 time 808s 13 (4.61%) aligned >1 times 808s 12.15% overall alignment rate 808s Flattened IUPAC characters 808s Mutating sequence Sim.pm.2 808s Introducing 9 SNPs, 0/2 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutating sequence Sim.pm.1 808s Introducing 2 SNPs, 0/0 ref/read gaps, and 0 rearrangements 808s Finished SNPs 808s Finished ref gaps 808s Finished read gaps 808s Mutated reference genome to subject genome 808s SNPs introduced: 11 808s Reference gaps introduced: 0 808s Read gaps introduced: 2 808s Rearrangements introduced: 0 808s Created read sampler 808s Sampling 80 reads 808s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 808s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 808s parsing sequence Sim.pm.1... 808s parsing sequence Sim.pm.2... 808s Parsed 78 reference bases 808s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 808s *** Run 98 of 100 808s /usr/bin/bowtie2 --mp 5.50901944156115,4.63018330073244 --nofw --cp-ival 1 -D 37 --trim3 3 --rdg 42.9665733506711 --rfg 14.6246661334749,19.4727699501372 --score-min L,8.73574790988983,9.94135182537833 --mm --large-index --cp-min 4 --np 3 -i L --trim5 9 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 808s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 808s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '2' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 808s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '7' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 808s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '12' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 808s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '16' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 808s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '20' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 808s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read '21' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 808s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '25' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 808s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '27' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 808s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '28' because it was < 2 characters long 808s Warning: skipping mate #2 of read '28' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 808s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '32' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 808s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '35' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 808s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '38' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 808s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '40' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 808s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '59' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 808s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '60' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 808s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '67' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 808s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '75' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 808s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '79' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 808s 80 reads; of these: 808s 62 (77.50%) were paired; of these: 808s 62 (100.00%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 0 (0.00%) aligned concordantly >1 times 808s ---- 808s 62 pairs aligned concordantly 0 times; of these: 808s 0 (0.00%) aligned discordantly 1 time 808s ---- 808s 62 pairs aligned 0 times concordantly or discordantly; of these: 808s 124 mates make up the pairs; of these: 808s 119 (95.97%) aligned 0 times 808s 5 (4.03%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 18 (22.50%) were unpaired; of these: 808s 15 (83.33%) aligned 0 times 808s 2 (11.11%) aligned exactly 1 time 808s 1 (5.56%) aligned >1 times 808s 5.63% overall alignment rate 808s Read 50 alignments... 808s Read 100 alignments... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s GG 808s GG 808s Processing line... 808s Processing line... 808s TGTC 808s TGTC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s CC 808s CC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s /usr/bin/bowtie2 --mp 5.50901944156115,4.63018330073244 --nofw --cp-ival 1 -D 37 --trim3 3 --rdg 42.9665733506711 --rfg 14.6246661334749,19.4727699501372 --score-min L,8.73574790988983,9.94135182537833 --mm --large-index --cp-min 4 --np 3 -i L --trim5 9 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s ACAACCCGAAC 808s ACAACCCGAAC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s TTG 808s TTG 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s CGTCG 808s CGTCG 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s GG 808s GG 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s TGACAACC 808s TGACAACC 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s Processing line... 808s --- Summary --- 808s Read 1 reference strings 808s Checked 8 alignments, 0 edits 808s --------------- 808s PASSED 808s ALSO checking that bowtie2 and bowtie2-align match up 808s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 808s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '2' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 808s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '7' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 808s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '12' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 808s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '16' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 808s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '20' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 808s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read '21' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 808s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '25' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 808s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '27' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 808s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '28' because it was < 2 characters long 808s Warning: skipping mate #2 of read '28' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 808s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '32' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 808s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '35' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 808s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '38' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 808s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '40' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 808s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '59' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 808s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '60' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 808s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '67' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 808s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '75' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 808s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '79' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 808s 80 reads; of these: 808s 62 (77.50%) were paired; of these: 808s 62 (100.00%) aligned concordantly 0 times 808s 0 (0.00%) aligned concordantly exactly 1 time 808s 0 (0.00%) aligned concordantly >1 times 808s ---- 808s 62 pairs aligned concordantly 0 times; of these: 808s 0 (0.00%) aligned discordantly 1 time 808s ---- 808s 62 pairs aligned 0 times concordantly or discordantly; of these: 808s 124 mates make up the pairs; of these: 808s 119 (95.97%) aligned 0 times 808s 5 (4.03%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 18 (22.50%) were unpaired; of these: 808s 15 (83.33%) aligned 0 times 808s 2 (11.11%) aligned exactly 1 time 808s 1 (5.56%) aligned >1 times 808s 5.63% overall alignment rate 808s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 808s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 808s /usr/bin/bowtie2 --mp 5.50901944156115,4.63018330073244 --nofw --cp-ival 1 -D 37 --trim3 3 --rdg 42.9665733506711 --rfg 14.6246661334749,19.4727699501372 --score-min L,8.73574790988983,9.94135182537833 --mm --large-index --cp-min 4 --np 3 -i L --trim5 9 -f -p 4 -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 808s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '2; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '2; setting to 0 instead 808s Warning: skipping mate #1 of read '2' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '2' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '4; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '6; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '7; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '7; setting to 0 instead 808s Warning: skipping mate #1 of read '7' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '7' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '8; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '9; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '10; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '11; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '12; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '12; setting to 0 instead 808s Warning: skipping mate #1 of read '12' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '12' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '13; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '14; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '15; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '16; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '16; setting to 0 instead 808s Warning: skipping mate #1 of read '16' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '16' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '17; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '18; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '20; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '20; setting to 0 instead 808s Warning: skipping mate #1 of read '20' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '20' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '21; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '21; setting to 0 instead 808s Warning: skipping mate #2 of read '21' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read '21' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '22; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '23; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '24; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 808s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '25' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '27; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '27; setting to 0 instead 808s Warning: skipping mate #1 of read '27' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '27' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '28; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '28; setting to 0 instead 808s Warning: skipping mate #1 of read '28' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #2 of read '28' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '28' because it was < 2 characters long 808s Warning: skipping mate #2 of read '28' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '29; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '32; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '32; setting to 0 instead 808s Warning: skipping mate #1 of read '32' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '32' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '33; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '33; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '35; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '35; setting to 0 instead 808s Warning: skipping mate #1 of read '35' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '35' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '36; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '36; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '37; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '37; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 808s Warning: skipping read '38' because length (0) <= # seed mismatches (0) 808s Warning: skipping read '38' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '39; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '39; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '40; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '40; setting to 0 instead 808s Warning: skipping mate #1 of read '40' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '40' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '41; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '41; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '45; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '45; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '46; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '46; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '47; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '47; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '48; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '48; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '50; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '50; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '51; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '51; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '52; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '52; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '53; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '53; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '54; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '54; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '55; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '55; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '56; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '56; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '57; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '57; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '58; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '58; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '59; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '59; setting to 0 instead 808s Warning: skipping mate #1 of read '59' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '59' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '60; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '60; setting to 0 instead 808s Warning: skipping mate #1 of read '60' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '60' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '61; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '61; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '63; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '63; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '65; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '65; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '67; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '67; setting to 0 instead 808s Warning: skipping mate #1 of read '67' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '67' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '69; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '69; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '70; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '70; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '71; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '71; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '72; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '72; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '73; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '73; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '74; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '74; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '75; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '75; setting to 0 instead 808s Warning: skipping mate #1 of read '75' because length (0) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '75' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '76; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '76; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '77; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '77; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '78; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '78; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '79; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '79; setting to 0 instead 808s Warning: skipping mate #1 of read '79' because length (1) <= # seed mismatches (0) 808s Warning: skipping mate #1 of read '79' because it was < 2 characters long 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #1 of read '80; setting to 0 instead 808s Warning: minimum score function gave positive number in --end-to-end mode for mate #2 of read '80; setting to 0 instead 809s 80 reads; of these: 809s 62 (77.50%) were paired; of these: 809s 62 (100.00%) aligned concordantly 0 times 809s 0 (0.00%) aligned concordantly exactly 1 time 809s 0 (0.00%) aligned concordantly >1 times 809s ---- 809s 62 pairs aligned concordantly 0 times; of these: 809s 0 (0.00%) aligned discordantly 1 time 809s ---- 809s 62 pairs aligned 0 times concordantly or discordantly; of these: 809s 124 mates make up the pairs; of these: 809s 119 (95.97%) aligned 0 times 809s 5 (4.03%) aligned exactly 1 time 809s 0 (0.00%) aligned >1 times 809s 18 (22.50%) were unpaired; of these: 809s 15 (83.33%) aligned 0 times 809s 2 (11.11%) aligned exactly 1 time 809s 1 (5.56%) aligned >1 times 809s 5.63% overall alignment rate 809s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 809s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 809s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 809s Flattened IUPAC characters 809s Mutating sequence Sim.pm.1 809s Introducing 4 SNPs, 0/0 ref/read gaps, and 0 rearrangements 809s Finished SNPs 809s Finished ref gaps 809s Finished read gaps 809s Mutating sequence Sim.pm.2 809s Introducing 4 SNPs, 0/1 ref/read gaps, and 2 rearrangements 809s Finished SNPs 809s Finished ref gaps 809s Finished read gaps 809s Mutated reference genome to subject genome 809s SNPs introduced: 8 809s Reference gaps introduced: 0 809s Read gaps introduced: 1 809s Rearrangements introduced: 2 809s Created read sampler 809s Sampling 98 reads 809s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fasta & /tmp/Sim.pm.ZMWIC0u__2.fasta 809s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 809s parsing sequence Sim.pm.1... 809s *** Run 99 of 100 809s /usr/bin/bowtie2 --nofw --mp 7.33100850374239,6.4076051575348 -N 0 -L25 --cp-ival 2 --local --mm --score-min L,3.95672023683843,2.47261099385653 --rdg 47.9889407768194 --rfg 17.2419647279042,18.1862011453263 -R 2 --cp-min 2 --large-index -M 6 --trim5 4 -f -x /tmp/Sim.pm.ZMWIC0u_ -1 /tmp/Sim.pm.ZMWIC0u__1.fasta -2 /tmp/Sim.pm.ZMWIC0u__2.fasta 809s parsing sequence Sim.pm.2... 809s Parsed 78 reference bases 809s Warning: -M is deprecated. Use -D and -R to adjust effort instead. 809s Warning: skipping mate #1 of read '5' because length (0) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '5' because it was < 2 characters long 809s Warning: skipping mate #2 of read '19' because length (1) <= # seed mismatches (0) 809s Warning: skipping mate #2 of read '19' because it was < 2 characters long 809s Warning: skipping mate #2 of read '20' because length (1) <= # seed mismatches (0) 809s Warning: skipping mate #2 of read '20' because it was < 2 characters long 809s Warning: skipping mate #1 of read '38' because length (0) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '38' because it was < 2 characters long 809s Warning: skipping mate #1 of read '43' because length (0) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '43' because it was < 2 characters long 809s Warning: skipping mate #1 of read '51' because length (0) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '51' because it was < 2 characters long 809s Warning: skipping mate #1 of read '70' because length (0) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '70' because it was < 2 characters long 809s Warning: skipping mate #1 of read '77' because length (0) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '77' because it was < 2 characters long 809s Read 50 alignments... 809s Warning: skipping mate #1 of read '88' because length (0) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '88' because it was < 2 characters long 809s Warning: skipping mate #2 of read '90' because length (1) <= # seed mismatches (0) 809s Warning: skipping mate #2 of read '90' because it was < 2 characters long 809s Warning: skipping mate #1 of read '96' because length (1) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '96' because it was < 2 characters long 809s Warning: skipping mate #1 of read '97' because length (0) <= # seed mismatches (0) 809s Warning: skipping mate #1 of read '97' because it was < 2 characters long 809s Read 100 alignments... 809s 98 reads; of these: 809s 89 (90.82%) were paired; of these: 809s 89 (100.00%) aligned concordantly 0 times 809s 0 (0.00%) aligned concordantly exactly 1 time 809s 0 (0.00%) aligned concordantly >1 times 809s ---- 809s 89 pairs aligned concordantly 0 times; of these: 809s 0 (0.00%) aligned discordantly 1 time 809s ---- 809s 89 pairs aligned 0 times concordantly or discordantly; of these: 809s 178 mates make up the pairs; of these: 809s 178 (100.00%) aligned 0 times 809s 0 (0.00%) aligned exactly 1 time 809s 0 (0.00%) aligned >1 times 809s 9 (9.18%) were unpaired; of these: 809s 9 (100.00%) aligned 0 times 809s 0 (0.00%) aligned exactly 1 time 809s 0 (0.00%) aligned >1 times 809s 0.00% overall alignment rate 809s Read 150 alignments... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s *** Run 100 of 100 809s /usr/bin/bowtie2 --large-index --cp-min 7 -i C,1.85033467005866,7.45273373438156 --trim5 3 --np 3 --norc --cp-ival 1 --mp 7.09268728731127,3.60796563126011 --nofw --rdg 26.1216287633118,18.7951596638135 --score-min L,6.67459912660575,9.36374144391996 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s --- Summary --- 809s Read 1 reference strings 809s Checked 0 alignments, 0 edits 809s --------------- 809s PASSED 809s Flattened IUPAC characters 809s Mutating sequence Sim.pm.1 809s Introducing 0 SNPs, 1/0 ref/read gaps, and 0 rearrangements 809s Finished SNPs 809s Finished ref gaps 809s Finished read gaps 809s Mutating sequence Sim.pm.2 809s Introducing 0 SNPs, 1/1 ref/read gaps, and 0 rearrangements 809s Finished SNPs 809s Finished ref gaps 809s Finished read gaps 809s Mutated reference genome to subject genome 809s SNPs introduced: 0 809s Reference gaps introduced: 2 809s Read gaps introduced: 1 809s Rearrangements introduced: 0 809s Created read sampler 809s Sampling 107 reads 809s Dumping reads to temporary files /tmp/Sim.pm.ZMWIC0u__1.fastq & /tmp/Sim.pm.ZMWIC0u__2.fastq 809s Parsing FASTA file /tmp/Sim.pm.ZMWIC0u_.fa... 809s parsing sequence Sim.pm.1... 809s parsing sequence Sim.pm.2... 809s Parsed 78 reference bases 809s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 809s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '1' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 809s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '16' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 809s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '25' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 809s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '28' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 809s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '39' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 809s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '47' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 809s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '48' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 809s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '49' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 809s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '51' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 809s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 809s Warning: skipping read '55' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 809s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '56' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 809s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '63' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 809s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '75' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 809s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '86' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 809s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '88' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 809s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '93' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 809s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '100' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 809s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '101' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 809s 107 reads; of these: 809s 107 (100.00%) were unpaired; of these: 809s 107 (100.00%) aligned 0 times 809s 0 (0.00%) aligned exactly 1 time 809s 0 (0.00%) aligned >1 times 809s 0.00% overall alignment rate 809s Read 50 alignments... 809s Read 100 alignments... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s /usr/bin/bowtie2 --large-index --cp-min 7 -i C,1.85033467005866,7.45273373438156 --trim5 3 --np 3 --norc --cp-ival 1 --mp 7.09268728731127,3.60796563126011 --nofw --rdg 26.1216287633118,18.7951596638135 --score-min L,6.67459912660575,9.36374144391996 -q -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.als 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s Processing line... 809s --- Summary --- 809s Read 1 reference strings 809s Checked 0 alignments, 0 edits 809s --------------- 809s PASSED 809s ALSO checking that bowtie2 and bowtie2-align match up 809s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 809s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '1' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 809s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '16' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 809s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '25' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 809s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '28' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 809s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '39' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 809s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '47' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 809s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '48' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 809s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '49' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 809s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '51' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 809s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 809s Warning: skipping read '55' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 809s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '56' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 809s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '63' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 809s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '75' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 809s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '86' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 809s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '88' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 809s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '93' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 809s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '100' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 809s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '101' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 809s 107 reads; of these: 809s 107 (100.00%) were unpaired; of these: 809s 107 (100.00%) aligned 0 times 809s 0 (0.00%) aligned exactly 1 time 809s 0 (0.00%) aligned >1 times 809s 0.00% overall alignment rate 809s diff -uw /tmp/Sim.pm.ZMWIC0u_.als /tmp/Sim.pm.ZMWIC0u_.debug.als 809s ALSO checking that bowtie2 and bowtie2 -p X w/ X > 1 match up 809s /usr/bin/bowtie2 --large-index --cp-min 7 -i C,1.85033467005866,7.45273373438156 --trim5 3 --np 3 --norc --cp-ival 1 --mp 7.09268728731127,3.60796563126011 --nofw --rdg 26.1216287633118,18.7951596638135 --score-min L,6.67459912660575,9.36374144391996 -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als 809s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 809s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '1' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 809s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '16' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 809s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '25' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 809s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '28' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 809s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '39' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 809s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '47' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 809s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '48' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 809s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '49' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 809s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '51' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 809s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 809s Warning: skipping read '55' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 809s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '56' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 809s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '63' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 809s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '75' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 809s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '86' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 809s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '88' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 809s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '93' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 809s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '100' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 809s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '101' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 809s 107 reads; of these: 809s 107 (100.00%) were unpaired; of these: 809s 107 (100.00%) aligned 0 times 809s 0 (0.00%) aligned exactly 1 time 809s 0 (0.00%) aligned >1 times 809s 0.00% overall alignment rate 809s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.px.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 809s sort -k 1,1 -n -k 2,2 -k 3,3 -k 4,4 < /tmp/Sim.pm.ZMWIC0u_.debug.als | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted 809s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als.sorted /tmp/Sim.pm.ZMWIC0u_.px.als.sorted 809s ALSO checking that bowtie2 and bowtie2 -p X --reorder w/ X > 1 match up 809s /usr/bin/bowtie2 --large-index --cp-min 7 -i C,1.85033467005866,7.45273373438156 --trim5 3 --np 3 --norc --cp-ival 1 --mp 7.09268728731127,3.60796563126011 --nofw --rdg 26.1216287633118,18.7951596638135 --score-min L,6.67459912660575,9.36374144391996 -q -p 2 -x /tmp/Sim.pm.ZMWIC0u_ --reorder /tmp/Sim.pm.ZMWIC0u__1.fastq | grep -v '^@PG' > /tmp/Sim.pm.ZMWIC0u_.px.reord.als 809s Warning: minimum score function gave positive number in --end-to-end mode for read '1; setting to 0 instead 809s Warning: skipping read '1' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '1' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '2; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '3; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '4; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '5; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '6; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '7; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '8; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '9; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '10; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '11; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '12; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '13; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '14; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '15; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '16; setting to 0 instead 809s Warning: skipping read '16' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '16' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '17; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '18; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '19; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '20; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '21; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '22; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '23; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '24; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '25; setting to 0 instead 809s Warning: skipping read '25' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '25' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '26; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '27; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '28; setting to 0 instead 809s Warning: skipping read '28' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '28' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '29; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '30; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '31; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '32; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '33; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '34; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '35; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '36; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '37; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '38; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '39; setting to 0 instead 809s Warning: skipping read '39' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '39' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '40; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '41; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '42; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '43; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '44; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '45; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '46; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '47; setting to 0 instead 809s Warning: skipping read '47' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '47' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '48; setting to 0 instead 809s Warning: skipping read '48' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '48' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '49; setting to 0 instead 809s Warning: skipping read '49' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '49' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '50; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '51; setting to 0 instead 809s Warning: skipping read '51' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '51' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '52; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '53; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '54; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '55; setting to 0 instead 809s Warning: skipping read '55' because length (1) <= # seed mismatches (0) 809s Warning: skipping read '55' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '56; setting to 0 instead 809s Warning: skipping read '56' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '56' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '57; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '58; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '59; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '60; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '61; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '62; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '63; setting to 0 instead 809s Warning: skipping read '63' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '63' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '64; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '65; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '66; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '67; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '68; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '69; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '70; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '71; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '72; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '73; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '74; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '75; setting to 0 instead 809s Warning: skipping read '75' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '75' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '76; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '77; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '78; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '79; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '80; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '81; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '82; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '83; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '84; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '85; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '86; setting to 0 instead 809s Warning: skipping read '86' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '86' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '87; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '88; setting to 0 instead 809s Warning: skipping read '88' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '88' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '89; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '90; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '91; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '92; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '93; setting to 0 instead 809s Warning: skipping read '93' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '93' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '94; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '95; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '96; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '97; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '98; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '99; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '100; setting to 0 instead 809s Warning: skipping read '100' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '100' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '101; setting to 0 instead 809s Warning: skipping read '101' because length (0) <= # seed mismatches (0) 809s Warning: skipping read '101' because it was < 2 characters long 809s Warning: minimum score function gave positive number in --end-to-end mode for read '102; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '103; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '104; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '105; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '106; setting to 0 instead 809s Warning: minimum score function gave positive number in --end-to-end mode for read '107; setting to 0 instead 809s 107 reads; of these: 809s 107 (100.00%) were unpaired; of these: 809s 107 (100.00%) aligned 0 times 809s 0 (0.00%) aligned exactly 1 time 809s 0 (0.00%) aligned >1 times 809s 0.00% overall alignment rate 809s diff -uw /tmp/Sim.pm.ZMWIC0u_.debug.als /tmp/Sim.pm.ZMWIC0u_.px.reord.als 809s PASSED 809s SUCCESS: help message was detected! 812s autopkgtest [08:34:26]: test run-unit-test: -----------------------] 836s autopkgtest [08:34:50]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 836s run-unit-test PASS 836s autopkgtest [08:34:50]: @@@@@@@@@@@@@@@@@@@@ summary 836s run-unit-test PASS 1659s Creating nova instance adt-noble-ppc64el-bowtie2-20240327-082054-juju-7f2275-prod-proposed-migration-environment-3-fe0deefa-2ed6-48a8-b6d9-6791046a4d48 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID 2c4a456c-136a-4a3a-993e-7f82eda3b6c0)... 1659s ERROR (CommandError): Unable to delete the specified server(s).